Analysis of ploidy and the patterns of amplified fragment length polymorphism and methylation sensitive amplified polymorphism in strawberry plants recovered from cryopreservation.

PubMed

Hao, Yu-Jin; You, Chun-Xiang; Deng, Xui-Xin

2002-01-01

Shoot-tips of 10 strawberry genotypes were successfully cryopreserved using a modified encapsulation-dehydration method. All genotypes survived cryopreservation with high survival and regeneration rates. Eight Joho single-bud sibling lines were established as a model system for genetic analysis. Although cytological examination found chromosomal variation in both non-cryopreserved and cryopreserved samples, the ploidy constitution remained relatively stable after cryopreservation. DNA samples digested with MseI and PstI were used for amplified fragmentation length polymorphism (AFLP) assay. In 16 primer combinations, only one, namely, PCCA-MCAG, detected one site where band pattern changed after cryopreservation, which might be contributed to the change in DNA methylation status at PstI recognition site. Methylation sensitive amplified polymorphism (MSAP) assay was carried out for further investigation on the influence of cryopreservation on DNA methylation status. It was found that cryopreservation induced a significant change in DNA methylation status.

Microsatellite primers for a species of South African everlasting daisy (Helichrysum odoratissimum; Gnaphalieae, Asteraceae)1

PubMed Central

Glennon, Kelsey L.; Cron, Glynis V.

2016-01-01

Premise of the study: Microsatellites were developed for the widespread Helichrysum odoratissimum (Asteraceae) to estimate gene flow across diploid populations and to test if gene flow occurs among other closely related lineages within this genus. Methods and Results: Ten primer pairs were developed and tested using populations across South Africa; however, only seven primer pairs were polymorphic for the target species. The seven polymorphic primers amplified di- and trinucleotide repeats with up to 16 alleles per locus among 125 diploid individuals used for analyses. Conclusions: These markers can be used to estimate gene flow among populations of known ploidy level of H. odoratissimum to test evolutionary hypotheses. Furthermore, these markers amplify successfully in other Helichrysum species, including the other three taxonomic Group 4 species, and therefore can be used to inform taxonomic work on these species. PMID:27213125

Prognostic markers for colorectal cancer: estimating ploidy and stroma

PubMed Central

Danielsen, H E; Hveem, T S; Domingo, E; Pradhan, M; Kleppe, A; Syvertsen, R A; Kostolomov, I; Nesheim, J A; Askautrud, H A; Nesbakken, A; Lothe, R A; Svindland, A; Shepherd, N; Novelli, M; Johnstone, E; Tomlinson, I; Kerr, R; Kerr, D J

2018-01-01

Abstract Background We report here the prognostic value of ploidy and digital tumour-stromal morphometric analyses using material from 2624 patients with early stage colorectal cancer (CRC). Patients and methods DNA content (ploidy) and stroma-tumour fraction were estimated using automated digital imaging systems and DNA was extracted from sections of formalin-fixed paraffin-embedded (FFPE) tissue for analysis of microsatellite instability. Samples were available from 1092 patients recruited to the QUASAR 2 trial and two large observational series (Gloucester, n = 954; Oslo University Hospital, n = 578). Resultant biomarkers were analysed for prognostic impact using 5-year cancer-specific survival (CSS) as the clinical end point. Results Ploidy and stroma-tumour fraction were significantly prognostic in a multivariate model adjusted for age, adjuvant treatment, and pathological T-stage in stage II patients, and the combination of ploidy and stroma-tumour fraction was found to stratify these patients into three clinically useful groups; 5-year CSS 90% versus 83% versus 73% [hazard ratio (HR) = 1.77 (95% confidence interval (95% CI): 1.13–2.77) and HR = 2.95 (95% CI: 1.73–5.03), P < 0.001]. Conclusion A novel biomarker, combining estimates of ploidy and stroma-tumour fraction, sampled from FFPE tissue, identifies stage II CRC patients with low, intermediate or high risk of CRC disease specific death, and can reliably stratify clinically relevant patient sub-populations with differential risks of tumour recurrence and may support choice of adjuvant therapy for these individuals. PMID:29293881

Development of 11 polymorphic microsatellite markers for the blackberry rust fungus Phragmidium violaceum

USDA-ARS?s Scientific Manuscript database

Eleven polymorphic microsatellite markers were developed for the Uredinales fungus Phragmidium violaceum, which causes leaf rust on European blackberry (Rubus fruticosus L. aggregate). Allele frequency ranged between two and seventeen alleles per locus with no evidence of linkage disequilibrium amon...

Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus).

PubMed

Ludwig, A; Belfiore, N M; Pitra, C; Svirsky, V; Jenneckens, I

2001-07-01

Sturgeon (order Acipenserformes) provide an ideal taxonomic context for examination of genome duplication events. Multiple levels of ploidy exist among these fish. In a novel microsatellite approach, data from 962 fish from 20 sturgeon species were used for analysis of ploidy in sturgeon. Allele numbers in a sample of individuals were assessed at six microsatellite loci. Species with approximately 120 chromosomes are classified as functional diploid species, species with approximately 250 chromosomes as functional tetraploid species, and with approximately 500 chromosomes as functional octaploids. A molecular phylogeny of the sturgeon was determined on the basis of sequences of the entire mitochondrial cytochrome b gene. By mapping the estimated levels of ploidy on this proposed phylogeny we demonstrate that (I) polyploidization events independently occurred in the acipenseriform radiation; (II) the process of functional genome reduction is nearly finished in species with approximately 120 chromosomes and more active in species with approximately 250 chromosomes and approximately 500 chromosomes; and (III) species with approximately 250 and approximately 500 chromosomes arose more recently than those with approximately 120 chromosomes. These results suggest that gene silencing, chromosomal rearrangements, and transposition events played an important role in the acipenseriform genome formation. Furthermore, this phylogeny is broadly consistent with previous hypotheses but reveals a highly supported oceanic (Atlantic-Pacific) subdivision within the Acipenser/Huso complex.

Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus).

PubMed Central

Ludwig, A; Belfiore, N M; Pitra, C; Svirsky, V; Jenneckens, I

2001-01-01

Sturgeon (order Acipenserformes) provide an ideal taxonomic context for examination of genome duplication events. Multiple levels of ploidy exist among these fish. In a novel microsatellite approach, data from 962 fish from 20 sturgeon species were used for analysis of ploidy in sturgeon. Allele numbers in a sample of individuals were assessed at six microsatellite loci. Species with approximately 120 chromosomes are classified as functional diploid species, species with approximately 250 chromosomes as functional tetraploid species, and with approximately 500 chromosomes as functional octaploids. A molecular phylogeny of the sturgeon was determined on the basis of sequences of the entire mitochondrial cytochrome b gene. By mapping the estimated levels of ploidy on this proposed phylogeny we demonstrate that (I) polyploidization events independently occurred in the acipenseriform radiation; (II) the process of functional genome reduction is nearly finished in species with approximately 120 chromosomes and more active in species with approximately 250 chromosomes and approximately 500 chromosomes; and (III) species with approximately 250 and approximately 500 chromosomes arose more recently than those with approximately 120 chromosomes. These results suggest that gene silencing, chromosomal rearrangements, and transposition events played an important role in the acipenseriform genome formation. Furthermore, this phylogeny is broadly consistent with previous hypotheses but reveals a highly supported oceanic (Atlantic-Pacific) subdivision within the Acipenser/Huso complex. PMID:11454768

Isolation and characterization of polymorphic microsatellite loci from Zelkova schneideriana Hand.-Mazz.

PubMed

Liu, H L; Zhang, R Q; Geng, M L; Zhu, J Y; Ma, J L

2014-12-03

Zelkova schneideriana is a highly valued hardwood species. An improved technique for isolating codominant compound microsatellite markers was used to develop simple sequence repeat markers for Z. schneideriana. A total of 12 microsatellite loci were identified. Overall, the number of alleles per locus ranged from 8-19, with an average of 11.75. Observed heterozygosity and expected heterozygosity values ranged from 0.109-0.709 and 0.832-0.929, respectively. Polymorphic information content is from 0.803-0.915, with an average of 0.854. These markers will be very important for future research related to the genetic diversity, population structure, patterns of gene flow, and mating system of this species.

Isolation and characterization of 21 polymorphic microsatellite loci in the Japanese dace (Tribolodon hakonensis)

USGS Publications Warehouse

Koizumi, Noriyuki; Quinn, Thomas W.; Park, Myeongsoo; Fike, Jennifer A.; Nishida, Kazuya; Takemura, Takeshi; Watabe, Keiji; Mori, Atsushi

2011-01-01

Twenty one polymorphic microsatellite loci for the Japanese dace (Tribolodon hakonensis) were isolated and characterized. The number of observed alleles per locus in 32 individuals ranged from 3 to 30. The observed and expected heterozygosities ranged from 0.125 to 0.969 and from 0.175 to 0.973, respectively. All loci conformed to Hardy–Weinberg equilibrium, no linkage disequilibrium was observed between pairs of loci and no loci showed evidence of null alleles. These microsatellite loci will be useful for investigating the intraspecific genetic variation and population structure of this species.

DNA content analysis of colorectal cancer defines a distinct ‘microsatellite and chromosome stable’ group but does not predict response to radiotherapy

PubMed Central

Fadhil, Wakkas; Kindle, Karin; Jackson, Darryl; Zaitoun, Abed; Lane, Nina; Robins, Adrian; Ilyas, Mohammad

2014-01-01

Colorectal cancers (CRC) are thought to have genetic instability in the form of either microsatellite instability (MSI) or chromosomal instability (CIN). Recently, tumours have been described without either MSI or CIN, that is, microsatellite and chromosome stable (MACS) CRCs. We investigated the (i) frequency of the MACS-CRCs and (ii) whether this genotype predicted responsiveness to neoadjuvant chemoradiotherapy. To examine the frequency of MACS-CRCs, DNA content (ploidy) was examined in 89 sporadic microsatellite-stable CRCs using flow cytometry. The tumours were also screened for mutations in KRAS/BRAF/TP53/PIK3CA by QMC-PCR. To examine the value of tumour ploidy in predicting response to chemoradiotherapy, DNA content was tested in a separate group of 62 rectal cancers treated with neoadjuvant chemoradiotherapy. Fifty-one of 89 CRCs (57%) were aneuploid and 38 (43%) were diploid. There was no significant association between mutations in TP53/KRAS/BRAF/PIK3CA and ploidy. Testing of association between mutations revealed only mutual exclusivity of KRAS/BRAF mutation (P < 0.001). Of the 62 rectal cancers treated with neoadjuvant chemoradiotherapy, 22 had responded (Mandard tumour regression grade 1/2) and 40 failed to respond (Grade 3–5). Twenty-five of 62 (40%) tumours were diploid, but there was no association between ploidy and response to therapy. We conclude that MACS-CRCs form a significant proportion of microsatellite-stable CRCs with a mutation profile overlapping that of CRCs with CIN. A diploid genotype does not, however, predict the responsiveness to radiotherapy. PMID:24456329

Isolation, characterization, and cross-species amplification of polymorphic microsatellite markers for Pilosocereus machrisii (Cactaceae).

PubMed

Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Moraes, Evandro M

2011-08-01

Microsatellite primers were developed in Pilosocereus machrisii, a columnar cactus with a patchy distribution in eastern tropical South America, to assess its genetic diversity and population structure. Eleven microsatellite markers were developed, of which one was monomorphic among 51 individuals from two populations. The number of alleles per polymorphic locus ranged from two to eight, and the total number of alleles was 57. From the 11 isolated loci, nine were successfully amplified in the other four Pilosocereus species. The results showed that these markers will be useful for studies of genetic diversity, patterns of gene flow, and population genetic structure in P. machrisii, as well as across other congeneric species.

Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

PubMed

Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

2010-02-01

Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

Is early-onset microsatellite and chromosomally stable colorectal cancer a hallmark of a genetic susceptibility syndrome?

PubMed

Kets, C M; van Krieken, J H J M; van Erp, P E J; Feuth, T; Jacobs, Y H A; Brunner, H G; Ligtenberg, M J L; Hoogerbrugge, N

2008-02-15

Most colorectal cancers show either microsatellite or chromosomal instability. A subset of colorectal cancers, especially those diagnosed at young age, is known to show neither of these forms of genetic instability and thus might have a distinct pathogenesis. Colorectal cancers diagnosed at young age are suggestive for hereditary predisposition. We investigate whether such early-onset microsatellite and chromosomally stable colorectal cancers are a hallmark of a genetic susceptibility syndrome. The ploidy status of microsatellite stable (familial) colorectal cancers of patients diagnosed before age 50 (n = 127) was analyzed in relation to the histopathological characteristics and family history. As a control the ploidy status of sporadic colorectal cancer, with normal staining of mismatch repair proteins, diagnosed at the age of 69 years or above (n = 70) was determined. A diploid DNA content was used as a marker for chromosomal stability. Within the group of patients with (familial) early onset microsatellite stable colorectal cancer the chromosomally stable tumors did not differ from chromosomally unstable tumors with respect to mean age at diagnosis, fulfillment of Amsterdam criteria or pathological characteristics. Segregation analysis did not reveal any family with microsatellite and chromosomally stable colorectal cancer in 2 relatives. The prevalence of microsatellite and chromosomally stable colorectal cancer was not significantly different for the early and late onset group (28 and 21%, respectively). We find no evidence that early-onset microsatellite and chromosomally stable colorectal cancer is a hallmark of a hereditary colorectal cancer syndrome. (c) 2007 Wiley-Liss, Inc.

Isolation and characterization of polymorphic microsatellite loci in the green leafhopper Empoasca vitis Goethe (Homoptera).

PubMed

Papura, D; Giresse, X; Chauvin, B; Caron, H; Delmotte, F; VAN Helden, M

2009-05-01

Eight dinucleotide microsatellite loci were isolated and characterized within the green leafhopper Empoasca vitis (Goethe) using an enrichment cloning procedure. Primers were tested on 171 individuals collected in the southwest of France from the vine plants. The identified loci were polymorphic, with allelic diversity ranging from two to 18 alleles per locus. Observed heterozygosities were from 0.021 to 0.760. These microsatellite markers should prove to be a useful tool for estimating the population genetic structure, host-plant specialization and migration capacity of this insect. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Polymorphic microsatellite DNA markers for the Florida manatee (Trichechus manatus latirostris)

USGS Publications Warehouse

Pause, K.C.; Nourisson, C.; Clark, A.; Kellogg, M.E.; Bonde, R.K.; McGuire, P.M.

2007-01-01

Florida manatees (Trichechus manatus latirostris) are marine mammals that inhabit the coastal waters and rivers of the southeastern USA, primarily Florida. Previous studies have shown that Florida manatees have low mitochondrial DNA variability, suggesting that nuclear DNA loci are necessary for discriminatory analyses. Here we report 10 polymorphic microsatellite loci with an average of 4.2 alleles per locus, and average heterozygosity of 50.1%. These loci have been developed for use in population studies, parentage assignment, and individual identification. ?? 2007 Blackwell Publishing Ltd.

Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism.

PubMed

Agha, S H; Pilla, F; Galal, S; Shaat, I; D'Andrea, M; Reale, S; Abdelsalam, A Z A; Li, M H

2008-06-01

Seven microsatellite markers were used to study genetic diversity of three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian (Maltese and Montefalcone) goat breeds. The microsatellites showed a high polymorphic information content (PIC) of more than 0.5 in most of the locus-breed combinations and indicated that the loci were useful in assessing within- and between-breed variability of domestic goat (Capra hircus). The expected heterozygosity of the breeds varied from 0.670 to 0.792. In the geographically wider distributed Egyptian Baladi breed there were indications for deviations from random breeding. Analysis of genetic distances and population structure grouped the three Egyptian goat breeds together, and separated them from the two Italian breeds. The studied Mediterranean breeds sampled from African and European populations seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations.

Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes

PubMed Central

Ananda, Guruprasad; Hile, Suzanne E.; Breski, Amanda; Wang, Yanli; Kelkar, Yogeshwar; Makova, Kateryna D.; Eckert, Kristin A.

2014-01-01

Interruptions of microsatellite sequences impact genome evolution and can alter disease manifestation. However, human polymorphism levels at interrupted microsatellites (iMSs) are not known at a genome-wide scale, and the pathways for gaining interruptions are poorly understood. Using the 1000 Genomes Phase-1 variant call set, we interrogated mono-, di-, tri-, and tetranucleotide repeats up to 10 units in length. We detected ∼26,000–40,000 iMSs within each of four human population groups (African, European, East Asian, and American). We identified population-specific iMSs within exonic regions, and discovered that known disease-associated iMSs contain alleles present at differing frequencies among the populations. By analyzing longer microsatellites in primate genomes, we demonstrate that single interruptions result in a genome-wide average two- to six-fold reduction in microsatellite mutability, as compared with perfect microsatellites. Centrally located interruptions lowered mutability dramatically, by two to three orders of magnitude. Using a biochemical approach, we tested directly whether the mutability of a specific iMS is lower because of decreased DNA polymerase strand slippage errors. Modeling the adenomatous polyposis coli tumor suppressor gene sequence, we observed that a single base substitution interruption reduced strand slippage error rates five- to 50-fold, relative to a perfect repeat, during synthesis by DNA polymerases α, β, or η. Computationally, we demonstrate that iMSs arise primarily by base substitution mutations within individual human genomes. Our biochemical survey of human DNA polymerase α, β, δ, κ, and η error rates within certain microsatellites suggests that interruptions are created most frequently by low fidelity polymerases. Our combined computational and biochemical results demonstrate that iMSs are abundant in human genomes and are sources of population-specific genetic variation that may affect genome stability. The

Single-tube tetradecaplex panel of highly polymorphic microsatellite markers < 1 Mb from F8 for simplified preimplantation genetic diagnosis of hemophilia A.

PubMed

Zhao, M; Chen, M; Tan, A S C; Cheah, F S H; Mathew, J; Wong, P C; Chong, S S

2017-07-01

Essentials Preimplantation genetic diagnosis (PGD) of severe hemophilia A relies on linkage analysis. Simultaneous multi-marker screening can simplify selection of informative markers in a couple. We developed a single-tube tetradecaplex panel of polymorphic markers for hemophilia A PGD use. Informative markers can be used for linkage analysis alone or combined with mutation detection. Background It is currently not possible to perform single-cell preimplantation genetic diagnosis (PGD) to directly detect the common inversion mutations of the factor VIII (F8) gene responsible for severe hemophilia A (HEMA). As such, PGD for such inversion carriers relies on indirect analysis of linked polymorphic markers. Objectives To simplify linkage-based PGD of HEMA, we aimed to develop a panel of highly polymorphic microsatellite markers located near the F8 gene that could be simultaneously genotyped in a multiplex-PCR reaction. Methods We assessed the polymorphism of various microsatellite markers located ≤ 1 Mb from F8 in 177 female subjects. Highly polymorphic markers were selected for co-amplification with the AMELX/Y indel dimorphism in a single-tube reaction. Results Thirteen microsatellite markers located within 0.6 Mb of F8 were successfully co-amplified with AMELX/Y in a single-tube reaction. Observed heterozygosities of component markers ranged from 0.43 to 0.84, and ∼70-80% of individuals were heterozygous for ≥ 5 markers. The tetradecaplex panel successfully identified fully informative markers in a couple interested in PGD for HEMA because of an intragenic F8 point mutation, with haplotype phasing established through a carrier daughter. In-vitro fertilization (IVF)-PGD involved single-tube co-amplification of fully informative markers with AMELX/Y and the mutation-containing F8 amplicon, followed by microsatellite analysis and amplicon mutation-site minisequencing analysis. Conclusions The single-tube multiplex-PCR format of this highly polymorphic

Development and Characterization of Polymorphic Microsatellite Markers for Sedum sarmentosum (Crassulaceae) and Their Cross-Species Transferability.

PubMed

Xu, Jing; Hou, Fu-Yuan; Wan, Ding-Rong; Wang, Sha; Xu, Dong-Mei; Yang, Guang-Zhong

2015-11-05

Sedum sarmentosum is an important Chinese medicinal herb that exhibits anti-inflammatory, anti-angiogenic and anti-nociceptive properties. However, little is known about its genetic background. The first set of 14 microsatellite markers were isolated and characterized for S. sarmentosum using an SSR-enriched library. Fourteen polymorphic microsatellite markers were acquired with satisfactory amplifications and a polymorphic pattern in 48 S. sarmentosum individuals. The number of alleles ranged from 3 to 15. The observed and expected heterozygosities varied from 0.0833 to 0.8750 and 0.2168 to 0.9063, respectively. Two loci showed significant departure from the Hardy-Weinberg equilibrium. Cross-species amplification was carried out in other Sedum species. High rates of cross-species amplification were observed. The transferability value ranged from 85.7% in S. lineare to 64.3% in S. ellacombianum. These markers will be valuable for studying the genetic variation, population structure and germplasm characterization of S. sarmentosum and related Sedum species.

Isolation and Characterization of Novel Polymorphic Microsatellite Markers for Cimex hemipterus F. (Hemiptera: Cimicidae).

PubMed

Seri Masran, Siti Nor Ain; Ab Majid, Abdul Hafiz

2018-05-04

Due to the growing public health and tourism awareness, Cimex hemipterus Fabricius (Hemiptera: Cimicidae) has gained a great interest in increasing reported infestation cases in tropical regions of the world, including Malaysia. Since the information on the molecular ecology and population biology of this species are tremendously lacking, the isolation and development of molecular markers can be used to determine its genetic structure. In this study, novel microsatellite primers isolated from enriched genomic libraries of C. hemipterus were developed using 454 Roche shotgun sequencing. Seven validated polymorphic microsatellite primers were consistently amplified and characterized from 70 tropical bed bugs collected from seven locations throughout Malaysia. The number of alleles per locus identified ranged from 6 to 14. Comparison of loci for overall and between population were done with mean observed and expected heterozygosity were determined at 0.320 and 0.814, 0.320 and 0.727, respectively. Polymorphic information criteria (PIC) valued the markers as highly informative as PIC >0.5. Overall population, they are possibly in Hardy-Weinberg equilibrium with loci Ch_09ttn, Ch_01dn, and Ch_13dn showing signs of a null allele. There were no scoring errors caused by stutter peaks, no large allele dropout was detected for all loci and showed no evidence of linkage disequilibrium. In conclusion, all seven molecular microsatellite markers identified can be beneficially used to gain more information on the population genetic structure and breeding patterns of C. hemipterus as well as the relationship of dispersal and infestation.

Isolation and characterization of polymorphic microsatellite loci in Spondias radlkoferi (Anacardiaceae)1

PubMed Central

Aguilar-Barajas, Esther; Sork, Victoria L.; González-Zamora, Arturo; Rocha-Ramírez, Víctor; Arroyo-Rodríguez, Víctor; Oyama, Ken

2014-01-01

• Premise of the study: Microsatellite markers were developed for Spondias radlkoferi to assess the impact of primate seed dispersal on the genetic diversity and structure of this important tree species of Anacardiaceae. • Methods and Results: Fourteen polymorphic loci were isolated from S. radlkoferi through 454 GS-FLX Titanium pyrosequencing of genomic DNA. The number of alleles ranged from three to 12. The observed and expected heterozygosities ranged from 0.382 to 1.00 and from 0.353 to 0.733, respectively. The amplification was also successful in S. mombin and two genera of Anacardiaceae: Rhus aromatica and Toxicodendron radicans. • Conclusions: These microsatellite loci will be useful to assess the genetic diversity and population structure of S. radlkoferi and related species, and will allow us to investigate the effects of seed dispersal by spider monkeys (Ateles geoffroyi) on the genetic structure and diversity of S. radlkoferi populations in a fragmented rainforest. PMID:25383270

Microsatellite DNA library for Caiman latirostris.

PubMed

Zucoloto, Rodrigo Barban; Verdade, Luciano Martins; Coutinho, Luiz Lehmann

2002-12-15

New genetic markers were characterized for the broad-snouted caiman (Caiman latirostris) by constructing libraries enriched for microsatellite DNA. Construction and characterization of these libraries are described in the present study. One microsatellite marker was developed from a (ACC-TGG)(n)enriched microsatellite DNA library, and 12 microsatellite markers were developed from a (AC-TG)(n)enriched microsatellite DNA library. These markers were tested in wild-caught animals, and these tests resulted in ten new polymorphic microsatellites for C. latirostris. Copyright 2002 Wiley-Liss, Inc.

Who cares about ploidy anyway

USDA-ARS?s Scientific Manuscript database

Potato breeders focus on ploidy because it impacts breeding methods and ultimately, genetic gains. This paper explains why ploidy it important. It begins with a brief history of cultivated potato from the perspective of ploidy. Then, I describe how we can make genetic improvements in potato by reduc...

Single nucleotide polymorphisms and microsatellites in the canine glutathione S-transferase pi 1 (GSTP1) gene promoter.

PubMed

Sacco, James; Mann, Sarah; Toral, Keller

2017-01-01

Genetic polymorphisms within the glutathione S-transferase P1 ( GSTP1 ) gene affect the elimination of toxic xenobiotics by the GSTP1 enzyme. In dogs, exposure to environmental chemicals that may be GSTP1 substrates is associated with cancer. The objectives of this study were to investigate the genetic variability in the GSTP1 promoter in a diverse population of 278 purebred dogs, compare the incidence of any variants found between breeds, and predict their effects on gene expression. To provide information on ancestral alleles, a number of wolves, coyotes, and foxes were also sequenced. Fifteen single nucleotide polymorphisms (SNPs) and two microsatellites were discovered. Three of these loci were only polymorphic in dogs while three other SNPs were unique to wolves and coyotes. The major allele at c.-46 is T in dogs but is C in the wild canids. The c.-185 delT variant was unique to dogs. The microsatellite located in the 5' untranslated region (5'UTR) was a highly polymorphic GCC tandem repeat, consisting of simple and compound alleles that varied in size from 10 to 22-repeat units. The most common alleles consisted of 11, 16, and 17-repeats. The 11-repeat allele was found in 10% of dogs but not in the other canids. Unequal recombination and replication slippage between similar and distinct alleles may be the mechanism for the multiple microsatellites observed. Twenty-eight haplotypes were constructed in the dog, and an additional 8 were observed in wolves and coyotes. While the most common haplotype acrossbreeds was the wild-type *1A(17), other prevalent haplotypes included *3A(11) in Greyhounds, *6A(16) in Labrador Retrievers, *9A(16) in Golden Retrievers, and *8A(19) in Standard Poodles. Boxers and Siberian Huskies exhibited minimal haplotypic diversity. Compared to the simple 16*1 allele, the compound 16*2 allele (found in 12% of dogs) may interfere with transcription factor binding and/or the stability of the GSTP1 transcript. Dogs and other canids exhibit

Isolation and Characterization of Polymorphic Microsatellite Markers from the Malaria Vector Anopheles fluviatilis Species T (Diptera: Culicidae).

PubMed

Lather, Manila; Sharma, Divya; Dang, Amita S; Adak, Tridibes; Singh, Om P

2015-05-01

Anopheles fluviatilis James is an important malaria vector in India, Pakistan, Nepal, and Iran. It has now been recognized as a complex of at least four sibling species-S, T, U, and V, among which species T is the most widely distributed species throughout India. The taxonomic status of these species is confusing owing to controversies prevailing in the literature. In addition, chromosomal inversion genotypes, which were considered species-diagnostic for An. fluviatilis species T, are unreliable due to the existence of polymorphism in some populations. To study the genetic diversity at population level, we isolated and characterized 20 microsatellite markers from microsatellite-enriched genomic DNA library of An. fluviatilis T, of which 18 were polymorphic while two were monomorphic. The number of alleles per locus among polymorphic markers ranged from 4 to 19, and values for observed and expected heterozygosities varied from 0.352 to 0.857 and from 0.575 to 0.933, respectively. Thirteen markers had cross-cryptic species transferability to species S and U of the Fluviatilis Complex. This study provides a promising genetic tool for the population genetic analyses of An. fluviatilis. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Development of Polymorphic Microsatellite Loci for Potato Wart from Next-Generation Sequence Data.

PubMed

Gagnon, Marie-Claude; van der Lee, Theo A J; Bonants, Peter J M; Smith, Donna S; Li, Xiang; Lévesque, C André; Bilodeau, Guillaume J

2016-06-01

Synchytrium endobioticum is the fungal agent causing potato wart disease. Because of its severity and persistence, quarantine measures are enforced worldwide to avoid the spread of this disease. Molecular markers exist for species-specific detection of this pathogen, yet markers to study the intraspecific genetic diversity of S. endobioticum were not available. Whole-genome sequence data from Dutch pathotype 1 isolate MB42 of S. endobioticum were mined for perfect microsatellite motifs. Of the 62 selected microsatellites, 21 could be amplified successfully and displayed moderate levels of polymorphism in 22 S. endobioticum isolates from different countries. Nineteen multilocus genotypes were observed, with only three isolates from Canada displaying identical profiles. The majority of isolates from Canada clustered genetically. In contrast, most isolates collected in Europe show no genetic clustering associated with their geographic origin. S. endobioticum isolates with the same pathotype displayed highly variable genotypes and none of the microsatellite markers correlated with a specific pathotype. The markers developed in this study can be used to assess intraspecific genetic diversity of S. endobioticum and allow track and trace of genotypes that will generate a better understanding of the migration and spread of this important fungal pathogen and support management of this disease.

Applications of Redwood Genotyping by Using Microsatellite Markers

Treesearch

Chris Brinegar; Dan Bruno; Ryan Kirkbride; Steven Glavas; Ingrid Udranszky

2007-01-01

A panel of polymorphic microsatellite markers have been developed in coast redwood (Sequoia sempervirens). Two loci in particular (Seq18D7-3 and Seq21E5) demonstrate the potential of microsatellite genotyping in the assessment of genetic diversity and inheritance in redwoods. The highly polymorphic Seq18D7-3 marker provided evidence for the planting...

Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae.

PubMed

Yang, Ji Y; Motilal, Lambert A; Dempewolf, Hannes; Maharaj, Kamaldeo; Cronk, Q C B

2011-12-01

Chloroplast microsatellites were developed in Theobroma cacao to examine the genetic diversity of cacao cultivars in Trinidad and Tobago. Nine polymorphic microsatellites were designed from the chloroplast genomes of two T. cacao accessions. These microsatellites were tested in 95 hybrid accessions from Trinidad and Tobago. An average of 2.9 alleles per locus was found. These chloroplast microsatellites, particularly the highly polymorphic pentameric repeat, were useful in assessing genetic variation in T. cacao. In addition, these markers should also prove to be useful for population genetic studies in other species of Malvaceae.

Eight polymorphic microsatellite loci for the Australian plague locust, Chortoicetes terminifera.

PubMed

Chapuis, Marie-Pierre; Popple, Julie-Anne; Simpson, Stephen J; Estoup, Arnaud; Martin, Jean-François; Steinbauer, Martin; McCulloch, Laurence; Sword, Gregory A

2008-11-01

Few population genetics studies have been carried out on major locust species. In particular, an understanding of the population genetic structure of the Australian plague locust, Chortoicetes terminifera, is lacking. We isolated and characterized eight polymorphic microsatellite loci in C. terminifera, and described experimental conditions for polymerase chain reaction multiplexing and genotyping these loci. The number of alleles per locus ranged from 11 to 29 and the expected heterozygosity ranged from 0.797 to 0.977. One locus was found to be X-linked. Results of cross-taxon amplification tests are reported in four species of the Oedipodinae subfamily. Journal compilation © 2008 Blackwell Publishing Ltd. No claim to original US government works.

Characterization of 12 polymorphic microsatellite markers for a facultatively eusocial sweat bee (Megalopta genalis).

PubMed

Kapheim, Karen M; Pollinger, John P; Wcislo, William T; Wayne, Robert K

2009-11-01

We developed a library of twelve polymorphic di- and tri-nucleotide microsatellite markers for Megalopta genalis, a facultatively eusocial sweat bee. We tested each locus in a panel of 23 unrelated females and found 7-20 alleles per locus. Observed and expected heterozygosities ranged from 0.65 to 0.96 and from 0.69 to 0.95 respectively. None of the loci deviated from Hardy-Weinberg equilibrium proportions or was found to be in gametic disequilibrium. © 2009 Blackwell Publishing Ltd.

Informative genomic microsatellite markers for efficient genotyping applications in sugarcane.

PubMed

Parida, Swarup K; Kalia, Sanjay K; Kaul, Sunita; Dalal, Vivek; Hemaprabha, G; Selvi, Athiappan; Pandit, Awadhesh; Singh, Archana; Gaikwad, Kishor; Sharma, Tilak R; Srivastava, Prem Shankar; Singh, Nagendra K; Mohapatra, Trilochan

2009-01-01

Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.

Microsatellite polymorphism in the P1 promoter region of the IGF-1 gene is associated with endometrial cancer

PubMed Central

KWASNIEWSKI, WOJCIECH; GOZDZICKA-JOZEFIAK, ANNA; WOLUN-CHOLEWA, MARIA; POLAK, GRZEGORZ; SIEROCINSKA-SAWA, JADWIGA; KWASNIEWSKA, ANNA; KOTARSKI, JAN

2016-01-01

Endometrial carcinoma (EC) is the most common type of gynecological malignancy. Studies have demonstrated that the insulin growth factor (IGF) pathway is implicated in the development of endometrial tumors and that the serum levels of IGF-1 are affected by estrogen. Most EC cells with high microsatellite instability (MSI-H) accumulate mutations at a microsatellite sequence in the IGF-1 gene. The present study investigated the CA repeat polymorphism in the P1 promoter region of the IGF-1 gene among Caucasian females with endometrial hyperplasia, EC and healthy control subjects, whose blood serum and surgical tissue specimens were analyzed. Differences or correlations between the analyzed parameters [serum levels of IGF-1 and IGF binding protein (IGFBP)-1 and IGFBP-3 as well as estrogens among the polymorphisms] were verified using the χ2, Mann-Whitney U, Kruskal-Wallis or Spearman's rank correlation tests. A PCR amplification and DNA sequencing analysis was used for identification of (CA)n repeats in the P1 region of IGF-1. ELISA was used to determine the blood serum levels of IGF-1, IGFBP-1, IGFBP-3 and estrogens. Furthermore, IGF-1 was assessed in endometrial tissues by immunohistochemical analysis. The present study indicated no statistically significant differences between serum levels of IGF-1, IGFBP-1, IGFBP-3 and estrone, estriol and estradiol in the control and study groups. A significant correlation was identified between the IGF-1 levels and estrone levels in the MSI-H polymorphism (r=−0.41, P=0.012) as well as a highly negative correlation between IGF-1 levels and the estradiol levels in the MSI-H polymorphism (r=−0.6, P=0.002). Genotypes without the 19 CA allele were predominantly found in EC. Furthermore, statistical analysis indicated that the number of IGF-1-expressing cells was significantly elevated in MSI-H type 18-20 (P= 0.0072), MSI-L type 19-20 (P=0.025) and microsatellite-stable MSS type 19-19 (P=0.024) compared with those in the MSI-H 20

Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections.

PubMed

Murray, Lee; Mobegi, Victor A; Duffy, Craig W; Assefa, Samuel A; Kwiatkowski, Dominic P; Laman, Eugene; Loua, Kovana M; Conway, David J

2016-05-12

In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers of SNPs. As expected, the number of microsatellite loci with more than one allele in each isolate was highly significantly inversely correlated with the genome-wide F ws fixation index (r = -0.88, P < 0.001). However, the microsatellite analysis revealed that most isolates contained mixed genotypes, even those that had no detectable genome sequence heterogeneity. Random sampling of different numbers of SNPs showed that an F ws index derived from ten or more SNPs with minor allele frequencies of >10 % had high correlation (r > 0.90) with the index derived using all SNPs. Different types of data give highly correlated indices of within-infection diversity, although PCR-based analysis detects low-level minority genotypes not apparent in bulk sequence analysis. When whole-genome data are not obtainable, quantitative assay of ten or more SNPs can yield a reasonably accurate estimate of the within-infection fixation index (F ws).

Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

USGS Publications Warehouse

Munguia-Vega, A.; Rodriguez-Estrella, R.; Nachman, M.; Culver, M.

2009-01-01

Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

Development and characterization of 33 novel polymorphic microsatellite markers for the brown tree snake Boiga irregularis.

PubMed

Unger, Shem D; Abernethy, Erin F; Lance, Stacey L; Beasley, Rochelle R; Kimball, Bruce A; McAuliffe, Thomas W; Jones, Kenneth L; Rhodes, Olin E

2015-11-07

Boiga irregularis is a widespread invasive species on Guam and has led to extirpation of most of the island's native avifauna. There are presently no microsatellite markers for this invasive species, hence we developed highly polymorphic microsatellite markers to allow for robust population genetic studies on Guam. We isolated and characterized 33 microsatellite loci for the brown tree snake, B. irregularis. The loci were screened across 32 individuals from Guam. The number of alleles per locus ranged from three to ten, with an average of 4.62. The expected (He) and observed heterozygosity (Ho) ranged from 0.294 to 0.856 and from 0.031 to 0.813, with an average of 0.648 and 0.524, respectively. Significant deviations from Hardy-Weinberg equilibrium were detected at seven loci after Bonferoni correction. Probability of identity values ranged from 0.043 to 0.539. These genetic markers are useful for understanding a suite of post-invasion population genetic parameters, sources of invasions, and effectiveness of management strategies for this invasive species.

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system.

PubMed

Huang, Jie; Li, Yu-Zhi; Du, Lian-Ming; Yang, Bo; Shen, Fu-Jun; Zhang, He-Min; Zhang, Zhi-He; Zhang, Xiu-Yue; Yue, Bi-Song

2015-02-07

The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda. By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What's more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system. The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual

Survey and Analysis of Microsatellites in the Silkworm, Bombyx mori

PubMed Central

Prasad, M. Dharma; Muthulakshmi, M.; Madhu, M.; Archak, Sunil; Mita, K.; Nagaraju, J.

2005-01-01

We studied microsatellite frequency and distribution in 21.76-Mb random genomic sequences, 0.67-Mb BAC sequences from the Z chromosome, and 6.3-Mb EST sequences of Bombyx mori. We mined microsatellites of ≥15 bases of mononucleotide repeats and ≥5 repeat units of other classes of repeats. We estimated that microsatellites account for 0.31% of the genome of B. mori. Microsatellite tracts of A, AT, and ATT were the most abundant whereas their number drastically decreased as the length of the repeat motif increased. In general, tri- and hexanucleotide repeats were overrepresented in the transcribed sequences except TAA, GTA, and TGA, which were in excess in genomic sequences. The Z chromosome sequences contained shorter repeat types than the rest of the chromosomes in addition to a higher abundance of AT-rich repeats. Our results showed that base composition of the flanking sequence has an influence on the origin and evolution of microsatellites. Transitions/transversions were high in microsatellites of ESTs, whereas the genomic sequence had an equal number of substitutions and indels. The average heterozygosity value for 23 polymorphic microsatellite loci surveyed in 13 diverse silkmoth strains having 2–14 alleles was 0.54. Only 36 (18.2%) of 198 microsatellite loci were polymorphic between the two divergent silkworm populations and 10 (5%) loci revealed null alleles. The microsatellite map generated using these polymorphic markers resulted in 8 linkage groups. B. mori microsatellite loci were the most conserved in its immediate ancestor, B. mandarina, followed by the wild saturniid silkmoth, Antheraea assama. PMID:15371363

Microsatellite primers for vulnerable seagrass Halophila beccarii (Hydrocharitaceae).

PubMed

Jiang, Kai; Shi, Yi-Su; Zhang, Jian; Xu, Na-Na

2011-06-01

Polymorphic microsatellite primers were developed in the vulnerable seagrass Halophila beccarii to investigate genetic variation and provide necessary markers for studying its population genetic structure. Six polymorphic and six monomorphic microsatellite loci were developed in H. beccarii. Most loci were successfully amplified across 40 H. beccarii individuals collected from three populations from coastal regions of southern China. Two to four alleles per locus were observed at the six polymorphic loci. The highest expected heterozygosity was 0.5737. The results demonstrate low levels of polymorphism in H. beccarii from coastal regions of southern China. They also illustrate that these primers may be useful for studying the mating system and population genetics of H. beccarii on a global scale.

Undermethylated DNA as a source of microsatellites from a conifer genome.

PubMed

Zhou, Y; Bui, T; Auckland, L D; Williams, C G

2002-02-01

Developing microsatellites from the large, highly duplicated conifer genome requires special tools. To improve the efficiency of developing Pinus taeda L. microsatellites, undermethylated (UM) DNA fragments were used to construct a microsatellite-enriched copy library. A methylation-sensitive restriction enzyme, McrBC, was used to enrich for UM DNA before library construction. Digested DNA fragments larger than 9 kb were then excised and digested with RsaI and used to construct nine dinucleotide and trinucleotide libraries. A total of 1016 microsatellite-positive clones were detected among 11 904 clones and 620 of these were unique. Of 245 primer sets that produced a PCR product, 113 could be developed as UM microsatellite markers and 70 were polymorphic. Inheritance and marker informativeness were tested for a random sample of 36 polymorphic markers using a three-generation outbred pedigree. Thirty-one microsatellites (86%) had single-locus inheritance despite the highly duplicated nature of the P. taeda genome. Nineteen UM microsatellites had highly informative intercross mating type configurations. Allele number and frequency were estimated for eleven UM microsatellites using a population survey. Allele numbers for these UM microsatellites ranged from 3 to 12 with an average of 5.7 alleles/locus. Frequencies for the 63 alleles were mostly in the low-common range; only 14 of the 63 were in the rare allele (q < 0.05) class. Enriching for UM DNA was an efficient method for developing polymorphic microsatellites from a large plant genome.

Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

PubMed Central

Jan, Catherine

2016-01-01

The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species. PMID:27688959

Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae).

PubMed

Jan, Catherine; Fumagalli, Luca

2016-01-01

The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

Comparing methods of ploidy estimation in potato.

USDA-ARS?s Scientific Manuscript database

Ploidy manipulation and the resulting need for rapid ploidy screening is an important part of a potato research and breeding program. Determining ploidy by counting chromosomes or measuring DNA in individual cells is definitive, but takes time, technical skills and equipment. We tested three predi...

Polymorphic Microsatellite Loci for Endemic Mussismilia Corals (Anthozoa: Scleractinia) of the Southwest Atlantic Ocean.

PubMed

Zilberberg, Carla; Peluso, Lívia; Marques, Jessica A; Cunha, Haydée

2014-01-01

In the Southwest Atlantic, coral reefs are unique due to their growth form, low species richness, and a high level of endemic coral species, which include the most important reef builders. Although these reefs are the only true biogenic reefs in the South Atlantic Ocean, population genetic studies are still lacking. The purpose of this study was to develop a suite of microsatellite loci to help gain insights into the population diversity and connectivity of the endemic scleractinian coral with the largest distributional range along the Southwest Atlantic coast, Mussismilia hispida Fourteen microsatellite loci were characterized, and their degree of polymorphism was analyzed in 33 individuals. The number of alleles varied between 4 and 17 per loci, and H o varied between 0.156 and 0.928, with 2 loci showing significant heterozygote deficiency. Cross-amplification tests on the other 2 species of the genus (Mussismilia braziliensis and Mussismilia harttii) demonstrated that these markers are suitable for studies of population diversity and structure of all 3 species of Mussismilia Because they are the most important reef builders in the Southwest Atlantic, the developed microsatellite loci may be important tools for connectivity and conservation studies of these endemic corals. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Restricted gene flow at the micro- and macro-geographical scale in marble trout based on mtDNA and microsatellite polymorphism.

PubMed

Pujolar, José M; Lucarda, Alvise N; Simonato, Mauro; Patarnello, Tomaso

2011-04-14

The genetic structure of the marble trout Salmo trutta marmoratus, an endemic salmonid of northern Italy and the Balkan peninsula, was explored at the macro- and micro-scale level using a combination of mitochondrial DNA (mtDNA) and microsatellite data. Sequence variation in the mitochondrial control region showed the presence of nonindigenous haplotypes indicative of introgression from brown trout into marble trout. This was confirmed using microsatellite markers, which showed a higher introgression at nuclear level. Microsatellite loci revealed a strong genetic differentiation across the geographical range of marble trout, which suggests restricted gene flow both at the micro-geographic (within rivers) and macro-geographic (among river systems) scale. A pattern of Isolation-by-Distance was found, in which genetic samples were correlated with hydrographic distances. A general West-to-East partition of the microsatellite polymorphism was observed, which was supported by the geographic distribution of mitochondrial haplotypes. While introgression at both mitochondrial and nuclear level is unlikely to result from natural migration and might be the consequence of current restocking practices, the pattern of genetic substructuring found at microsatellites has been likely shaped by historical colonization patterns determined by the geological evolution of the hydrographic networks.

Characterization and application of newly developed polymorphic microsatellite markers in the Ezo red fox (Vulpes vulpes schrencki).

PubMed

Tada, T; Seki, Y; Kameyama, Y; Kikkawa, Y; Wada, K

2016-12-19

The Ezo red fox (Vulpes vulpes schrencki), a subspecies endemic to Hokkaido island, Japan, is a known host species for the tapeworm Echinococcus multilocularis. To develop tools for molecular ecological studies, we isolated 28 microsatellite regions from the genome of Ezo red fox, and developed 18 polymorphic microsatellite markers. These markers were characterized using 7 individuals and 22 fecal samples of the Ezo red fox. The number of alleles for these markers ranged from 1 to 7, and the observed heterozygosity, estimated on the basis of the genotypes of 7 individuals, ranged from 0.29 to 1.00. All markers, except DvNok5, were in Hardy-Weinberg equilibrium (P > 0.05), and no linkage disequilibrium was detected among these loci, except between DvNok14 and DvNok28 (P = 0.01). Moreover, six microsatellite loci were successfully genotyped using feces-derived DNA from the Ezo red fox. The markers developed in our study might serve as a useful tool for molecular ecological studies of the Ezo red fox.

Genetic profiling of Trypanosoma cruzi directly in infected tissues using nested PCR of polymorphic microsatellites.

PubMed

Valadares, Helder Magno Silva; Pimenta, Juliana Ramos; de Freitas, Jorge Marcelo; Duffy, Tomás; Bartholomeu, Daniella C; Oliveira, Riva de Paula; Chiari, Egler; Moreira, Maria da Consolação Vieira; Filho, Geraldo Brasileiro; Schijman, Alejandro Gabriel; Franco, Glória Regina; Machado, Carlos Renato; Pena, Sérgio Danilo Junho; Macedo, Andréa Mara

2008-06-01

The investigation of the importance of the genetics of Trypanosoma cruzi in determining the clinical course of Chagas disease will depend on precise characterisation of the parasites present in the tissue lesions. This can be adequately accomplished by the use of hypervariable nuclear markers such as microsatellites. However the unilocal nature of these loci and the scarcity of parasites in chronic lesions make it necessary to use high sensitivity PCR with nested primers, whose design depends on the availability of long flanking regions, a feature not hitherto available for any known T. cruzi microsatellites. Herein, making use of the extensive T. cruzi genome sequence now available and using the Tandem Repeats Finder software, it was possible to identify and characterise seven new microsatellite loci--six composed of trinucleotide (TcTAC15, TcTAT20, TcAAT8, TcATT14, TcGAG10 and TcCAA10) and one composed of tetranucleotide (TcAAAT6) motifs. All except the TcCAA10 locus were physically mapped onto distinct intergenic regions of chromosome III of the CL Brener clone contigs. The TcCAA10 locus was localised within a hypothetical protein gene in the T. cruzi genome. All microsatellites were polymorphic and useful for T. cruzi genetic variability studies. Using the TcTAC15 locus it was possible to separate the strains belonging to the T. cruzi I lineage (DTU I) from those belonging to T. cruzi II (DTU IIb), T. cruzi III (DTU IIc) and a hybrid group (DTU IId, IIe). The long flanking regions of these novel microsatellites allowed construction of nested primers and the use of full nested PCR protocols. This strategy enabled us to detect and differentiate T. cruzi strains directly in clinical specimens including heart, blood, CSF and skin tissues from patients in the acute and chronic phases of Chagas disease.

High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species

PubMed Central

2013-01-01

Background Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient “off-the-shelf” markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. Results We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. Conclusions When combined with previously described conserved loci, this new set of conserved markers will not only

Polymorphic microsatellite markers for the endangered fish, the slender shiner Pseudopungtungia tenuicorpa and cross-species amplification across five related species.

PubMed

Kim, K S; Moon, S J; Han, S H; Kim, K Y; Bang, I C

2016-09-02

The slender shiner Pseudopungtungia tenuicorpa (Cypriniformes; Cyprinidae; Gobioninae) is an endangered freshwater fish species endemic to Korea. The current strategies for its conservation involve the study of population genetic characters and identification of management units. These strategies require suitable molecular markers to study genetic diversity and genetic structure. Here, we developed nine polymorphic microsatellite markers for P. tenuicorpa for the first time by applying an enrichment method from a size-selected genomic library. The developed microsatellite markers produced a total of 101 alleles (average 11.2). The observed and expected heterozygosities averaged 0.805 and 0.835, respectively. Among the nine identified markers, five markers showed successful amplification across five related Korean Gobioninae species. Thus, the microsatellite markers developed in this study will be useful to establish conservation strategies for both P. tenuicorpa and other related species.

Microsatellites as targets of natural selection.

PubMed

Haasl, Ryan J; Payseur, Bret A

2013-02-01

The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to selection that targets single nucleotide variants, fundamentally different types of mutation generate abundant polymorphism in genomes. Moreover, recent empirical results suggest that mutationally complex, multiallelic loci including microsatellites and copy number variants are sometimes targeted by natural selection. Given their abundance, the lack of inference methods tailored to the mutational peculiarities of these types of loci represents a notable gap in our ability to interrogate genomes for signatures of natural selection. Previous theoretical investigations of mutation-selection balance at multiallelic loci include assumptions that limit their application to inference from empirical data. Focusing on microsatellites, we assess the dynamics and population-level consequences of selection targeting mutationally complex variants. We develop general models of a multiallelic fitness surface, a realistic model of microsatellite mutation, and an efficient simulation algorithm. Using these tools, we explore mutation-selection-drift equilibrium at microsatellites and investigate the mutational history and selective regime of the microsatellite that causes Friedreich's ataxia. We characterize microsatellite selective events by their duration and cost, note similarities to sweeps from standing point variation, and conclude that it is premature to label microsatellites as ubiquitous agents of efficient adaptive change. Together, our models and simulation algorithm provide a powerful framework for statistical inference, which can be used to test the neutrality of microsatellites and other multiallelic variants.

Microsatellites as Targets of Natural Selection

PubMed Central

Haasl, Ryan J.; Payseur, Bret A.

2013-01-01

The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to selection that targets single nucleotide variants, fundamentally different types of mutation generate abundant polymorphism in genomes. Moreover, recent empirical results suggest that mutationally complex, multiallelic loci including microsatellites and copy number variants are sometimes targeted by natural selection. Given their abundance, the lack of inference methods tailored to the mutational peculiarities of these types of loci represents a notable gap in our ability to interrogate genomes for signatures of natural selection. Previous theoretical investigations of mutation-selection balance at multiallelic loci include assumptions that limit their application to inference from empirical data. Focusing on microsatellites, we assess the dynamics and population-level consequences of selection targeting mutationally complex variants. We develop general models of a multiallelic fitness surface, a realistic model of microsatellite mutation, and an efficient simulation algorithm. Using these tools, we explore mutation-selection-drift equilibrium at microsatellites and investigate the mutational history and selective regime of the microsatellite that causes Friedreich’s ataxia. We characterize microsatellite selective events by their duration and cost, note similarities to sweeps from standing point variation, and conclude that it is premature to label microsatellites as ubiquitous agents of efficient adaptive change. Together, our models and simulation algorithm provide a powerful framework for statistical inference, which can be used to test the neutrality of microsatellites and other multiallelic variants. PMID:23104080

Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.).

PubMed

Witsenboer, H; Michelmore, R W; Vogel, J

1997-12-01

Selectively amplified microsatellite polymorphic locus (SAMPL) analysis is a method of amplifying microsatellite loci using generic PCR primers. SAMPL analysis uses one AFLP primer in combination with a primer complementary to microsatellite sequences. SAMPL primers based on compound microsatellite sequences provided the clearest amplification patterns. We explored the potential of SAMPL analysis in lettuce to detect PCR-based codominant microsatellite markers. Fifty-eight SAMPLs were identified and placed on the genetic map. Seventeen were codominant. SAMPLs were dispersed with RFLP markers on 11 of the 12 main linkage groups in lettuce, indicating that they have a similar genomic distribution. Some but not all fragments amplified by SAMPL analysis were confirmed to contain microsatellite sequences by Southern hybridization. Forty-five cultivars of lettuce and five wild species of Lactuca were analyzed to determine the allelic diversity for codominant SAMPLs. From 3 to 11 putative alleles were found for each SAMPL; 2-6 alleles were found within Lactuca sativa and 1-3 alleles were found among the crisphead genotypes, the most genetically homogeneous plant type of L. sativa. This allelic diversity is greater than that found for RFLP markers. Numerous new alleles were observed in the wild species; however, there were frequent null alleles. Therefore, SAMPL analysis is more applicable to intraspecific than to interspecific comparisons. A phenetic analysis based on SAMPLs resulted in a dendrogram similar to those based on RFLP and AFLP markers.

Polymorphisms in mismatch repair genes are associated with risk and microsatellite instability of gastric cancer, and interact with life exposures.

PubMed

Zhu, Haifeng; Li, Xiaoqin; Zhang, Xiaomei; Chen, Deyu; Li, Dan; Ren, Jin; Gu, Hangang; Shu, Yongqian; Wang, Deqiang

2016-03-15

Epigenetic alterations of DNA mismatch repair (MMR) genes are associated with risk of gastric cancer (GC) by causing microsatellite instability (MSI). Less understood is the association of common polymorphisms in MMR genes with the risk and MSI phenotype of GC. A hospital-based study was conducted in China with 423 cases and 454 matched controls. Four potentially functional polymorphisms were selected and analyzed: rs1800734 in MLH1, rs2303428 in MSH2, rs735943 in EXO1, and rs11797 in TREX1. The rs1800734 G-allele was associated with decreased risk of GC (GA or GG vs AA, OR=0.72; 95% CI: 0.50-1.05; Ptrend=0.029). For combined effects, a dose-response manner was observed in which GC risk was increased with increasing number of at-risk genotypes (Ptrend=0.039); this manner mainly existed in MSI GC (Ptrend=0.047) rather than in microsatellite stability GC, though neither single polymorphism was linked with MSI. For exposures, modified effects were observed from green tea drinking and soy foods intake on rs11797 (P for interaction=0.007 and 0.016, respectively). The MLH1 rs1800734 polymorphism is associated with GC risk. Those at-risk genotypes have a joint effect on GC risk, which contributes to the MSI phenotype of GC. Life exposures modify GC risk, stratified by MMR genotypes. Copyright © 2015 Elsevier B.V. All rights reserved.

Polymorphisms of HLA microsatellite marker in Tunisian pemphigus foliaceus.

PubMed

Abida, O; Mahfoudh, N; Kammoun, A; Gaddour, L; Hakim, F; Toumi, A; Masmoudi, A; Ben Ayed, M; Turki, H; Masmoudi, H; Makni, H

2013-01-01

Pemphigus foliaceus (PF) is an autoimmune blistering skin disease that partly results from genetic factors, especially from human leucocyte antigen (HLA) class II genes. Several data have reported the involvement of microsatellite (STR) markers across different regions of the HLA in many auto-immune diseases. To test the hypothesis of the existence of a major HLA haplotype predisposing to PF, we analyzed six polymorphisms of microsatellite loci at 6p21.3-21.4 spanning HLA: D6S291, D6S273, TNFa, MICA, D6S265 and D6S276 in 81 PF patients compared to 123 healthy individuals recruited from the south of Tunisia. In this study, after Bonferroni's correction, 3 STR alleles from the TNFa locus were associated with the disease: the allele TNFa(∗)2 (p(c) = 4.2×10(-6)) and, at a lower level, the TNFa(∗)5 (p(c) = 0.014) as susceptibility alleles and TNFa(∗)6 (p(c) = 0.014) as protective ones. Furthermore, the expression of the TNFa(∗)2/TNFa(∗)5 genotype seem to confer susceptibility to PF (p = 0.00001, OR = 11.25). Interestingly, no significant LD was found between TNFa2/TNFa5 alleles and DRB1(∗)03/DRB1(∗)04 alleles. However, the multivariant regression analysis indicates that both the HLA class II and the TNFa alleles remained significant (p < 0.001). Although, these findings rejected our hypothesis on the existence of HLA susceptibility haplotype, they assessed the role of TNFa loci. Accordingly, TNFa seem to contribute to the aethiopathogenesis of Tunisian endemic PF may be by the induction of a high TNFα production which is known to enhance the autoimmune cascade of the disease. Copyright © 2012 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Isolation and characterization of 23 polymorphic microsatellite loci for a West Indian iguana (Cyclura pinguis) from the British Virgin Islands.

PubMed

Lau, Jennie; Alberts, Allison C; Chemnick, Leona G; Gerber, Glenn P; Jones, Kenneth C; Mitchell, Adele A; Ryder, Oliver A

2009-09-01

Twenty-three polymorphic microsatellite markers were identified and characterized for Cyclura pinguis, a critically endangered species of lizard (Sauria: Iguanidae) native to Anegada Island in the British Virgin Islands. We examined variation at these loci for 39 C. pinguis, finding up to five alleles per locus and an average expected heterozygosity of 0.55. Allele frequency estimates for these microsatellite loci will be used to characterize genetic diversity of captive and wild C. pinguis populations and to estimate relatedness among adult iguanas at the San Diego Zoo that form the nucleus of a captive breeding programme for this critically endangered species. © 2009 Blackwell Publishing Ltd.

Isolation and characterization of microsatellite Loci for Cornus sanguniea (Cornaceae) 1

USDA-ARS?s Scientific Manuscript database

Premise of the study: Microsatellite loci were developed for Cornus sanguinea and will permit genetic and conservation studies of the species. Methods and Results: A microsatellite-enriched library was used to develop 16 polymorphic microsatellite loci for C. sanguinea. The loci amplified 5-11 allel...

Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)1

USDA-ARS?s Scientific Manuscript database

Premise of the study: Microsatellite loci were developed for the endangered species Pityopsis ruthii and will permit genetic and conservation studies of the species. Methods and Results:A microsatellite enriched library was used to develop 12 polymorphic microsatellite loci for P. ruthii. The loci ...

PERMANENT GENETIC RESOURCES: Isolation and characterization of polymorphic microsatellite loci in common evening primrose (Oenothera biennis).

PubMed

Larson, E L; Bogdanowicz, S M; Agrawal, A A; Johnson, M T J; Harrison, R G

2008-03-01

We developed nine polymorphic microsatellite loci for evening primrose (Oenothera biennis). These loci have two to 18 alleles per locus and observed heterozygosities ranging from 0 to 0.879 in a sample of 34 individuals. In a pattern consistent with the functionally asexual reproductive system of this species, 17/36 pairs of loci revealed significant linkage disequilibrium and three loci showed significant deviations from Hardy-Weinberg equilibrium. The loci will be informative in identifying genotypes in multigenerational field studies to assess changes in genotype frequencies. © 2007 The Authors.

Microsatellite DNA capture from enriched libraries.

PubMed

Gonzalez, Elena G; Zardoya, Rafael

2013-01-01

Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.

Binary and microsatellite polymorphisms of the Y-chromosome in the Mbenzele pygmies from the Central African Republic.

PubMed

Coia, Valentina; Caglià, Alessandra; Arredi, Barbara; Donati, Francesco; Santos, Fabrício R; Pandya, Arpita; Taglioli, Luca; Paoli, Giorgio; Pascali, Vincenzo; Spedini, Gabriella; Destro-Bisol, Giovanni; Tyler-Smith, Chris

2004-01-01

This study analyzes the variation of six binary polymorphisms and six microsatellites in the Mbenzele Pygmies from the Central African Republic. Five different haplogroups (B2b, E(xE3a), E3a, P and BR(xB2b,DE,P)) were observed, with frequencies ranging from 0.022 (haplogroup P) to 0.609 (haplogroup E3a). A comparison of haplogroup frequencies indicates a close genetic affinity between the Mbenzele and the Biaka Pygmies, a finding consistent with the common origin and the geographical proximity of the two populations. The haplogroups P, BR(xB2b,DE,P) and E(xE3a), which are rare in sub-Saharan Africa but common in western Eurasia, were observed with frequencies ranging from 0.022 (haplogroup P) to 0.087 (haplogroup E(xE3a)). Thirty different microsatellite haplotypes were detected, with frequencies ranging from 0.022 to 0.152. The Mbenzele share the highest percent of microsatellite haplotypes with the Biaka Pygmies. Five out seven haplotypes which are shared by the Mbenzele and Biaka Pygmies belong to haplogroup E3a, which suggests that they are of Bantu origin. The plot based on F(st) genetic distances calculated using microsatellite data provides a picture of population relationships which is in part congruent and in part complementary to that obtained using haplogroup frequencies. Finally, the Mbenzele and Biaka Pygmies were found to be markedly more genetically similar using Y-chromosomal than autosomal microsatellites. We suggest that this could be due to the higher phylogenetic stability of Y-chromosome and to the effect of the male-biased gene flow during the Bantu expansion. Copyright 2003 Wiley-Liss, Inc.

Microsatellite markers for Senna spectabilis var. excelsa (Caesalpinioideae, Fabaceae)1

PubMed Central

López-Roberts, M. Cristina; Barbosa, Ariane R.; Paganucci de Queiroz, Luciano; van den Berg, Cássio

2016-01-01

Premise of the study: Senna spectabilis var. excelsa (Fabaceae) is a South and Central American tree of great ecological importance and one of the most common species in several sites of seasonally dry forests. Our goal was to develop microsatellite markers to assess the genetic diversity and structure of this species. Methods and Results: We designed and assessed 53 loci obtained from a microsatellite-enriched library and an intersimple sequence repeat library. Fourteen loci were polymorphic, and they presented a total of 39 alleles in a sample of 61 individuals from six populations. The mean values of observed and expected heterozygosities were 0.355 and 0.479, respectively. Polymorphism information content was 0.390 and the Shannon index was 0.778. Conclusions: Polymorphism information content and Shannon index indicate that at least nine of the 14 microsatellite loci developed are moderate to highly informative, and potentially useful for population genetic studies in this species. PMID:26819856

Development of eight polymorphic microsatellites for a Zn/Cd hyperaccumulator Sedum alfredii Hance (Crassulaceae).

PubMed

Huang, Hui-Run; Shu, Wen-Sheng; Mao, Zhi-Bin; Ge, Xue-Jun

2008-09-01

Sedum alfredii is a Zn/Cd hyperaccumulator distributed in East Asia. A total of eight polymorphic microsatellite markers were developed. These loci were screened in 25 individuals from one heavy metal-tolerant population and one nontolerant population, respectively. The average allele number of these markers was 5.25 per locus, ranging from two to nine. Population-specific alleles were found at each locus. The observed and expected heterozygosities ranged from 0.000 to 0.640 and from 0.451 to 0.819. Significant deviation from Hardy-Weinberg equilibrium was detected at both the species and the population level. No significant linkage disequilibrium was detected at population level. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Microsatellite analysis of Fasciola spp. in Egypt.

PubMed

Dar, Yasser; Amer, Said; Courtioux, Bertrand; Dreyfuss, Gilles

2011-12-01

Recently, the topic of diversity in Fasciola population in Egypt is controversial. The present study was performed to study the genetic diversity of isolated flukes based on microsatellites markers. Fasciola worms were collected from different hosts and geographical locations in Egypt. Control samples of Fasciola hepatica from France as well as Fasciola gigantica from Cameroon were included in the study. Collected flukes were identified morphologically and subjected for analysis using four microsatellite markers. Results of microsatellite profile (FM1 and FM2) proved that both species of Fasciola are distributed in Egypt irrespective of geographical location and host. Nevertheless, the microsatellite profile of some analyzed loci (FM2 and FM3) proved that Egyptian flukes showed more alleles compared to the reference ones. Differences of microsatellite profile in Egyptian isolates than that of corresponding reference samples indicate the remarkable diversity of these isolates. The present results highlighted the utility of microsatellite profile to discriminate between Fasciola species and to elucidate the diversity within the species. To our knowledge, this is the first time to study microsatellite polymorphism in Fasciola populations in Egypt.

Development of microsatellite markers for Dimorphandra mollis (Leguminosae), a widespread tree from the Brazilian cerrado.

PubMed

Souza, Helena A V; Collevatti, Rosane G; Lemos-Filho, José P; Santos, Fabrício R; Lovato, Maria Bernadete

2012-03-01

Microsatellite markers were developed for Dimorphandra mollis (Leguminosae), a widespread tree in the Brazilian cerrado (a savanna-like vegetation). Microsatellite markers were developed from an enriched library. The analyses of polymorphism were based on 56 individuals from three populations. Nine microsatellite loci were polymorphic, with the number of alleles per locus ranging from three to 10 across populations. The observed and expected heterozygosities per locus and population ranged from 0.062 to 0.850 and from 0.062 to 0.832, respectively. These microsatellites provide an efficient tool for population genetics studies and will be used to assess the genetic diversity and spatial genetic structure of D. mollis.

Isolation and Characterization of Microsatellite Loci for Cotesia plutellae (Hymenoptera: Braconidae)

PubMed Central

Liu, Tiansheng; Ke, Fushi; You, Shijun; Chen, Wenbin; He, Weiyi; You, Minsheng

2017-01-01

Fourteen polymorphic microsatellite loci were isolated in this transcriptome-based data analysis for Cotesia plutellae, which is an important larval parasitoid of the worldwide pest Plutella xylostella. A subsequent test was performed for a wild C. plutellae population (N = 32) from Fuzhou, Fujian, southeastern China, to verify the effectiveness of the 14 microsatellite loci in future studies on C. plutellae genetic diversity. The observed number of alleles ranged from two to six. The expected and observed heterozygosity ranged from 0.123 to 0.316 and from 0.141 to 0.281, respectively. The polymorphism information content (PIC) value ranged from 0.272 to 0.622. Potentially due to the substructure of the sampled population, three of the 14 microsatellite loci deviated from Hardy—Weinberg equilibrium (HWE). Further, loci C6, C22, and C31 could be amplified in Cocobius fulvus and Encarsia japonica, suggesting the transferability of these three polymorphic loci to other species of Hymenoptera. PMID:28632152

Novel microsatellite loci for Agave parryi and cross-amplification in Agave palmeri (Agavaceae).

PubMed

Lindsay, Denise L; Edwards, Christine E; Jung, Michael G; Bailey, Pamela; Lance, Richard F

2012-07-01

To examine the foraging behavior of nectarivorous bats in southeastern Arizona, we developed microsatellite primers in Agave parryi. These markers were also tested for cross-amplification and applicability to assess patterns of genetic diversity and structure in A. palmeri. Utilizing DNA sequence data from 454 shotgun sequencing, we identified seven novel polymorphic microsatellite loci in A. parryi and screened them for cross-amplification in A. palmeri. These markers were characterized in two populations of 30 individuals each for each species. In A. parryi, all primers were polymorphic and amplified between three and 12 alleles per population. In A. palmeri, all primers amplified, six were polymorphic, and allelic diversity ranged from one to 16 alleles per population. Our results demonstrate the applicability of these microsatellite primers for population genetics studies in both A. parryi and A. palmeri.

Characterization of 10 new nuclear microsatellite markers in Acca sellowiana (Myrtaceae).

PubMed

Klabunde, Gustavo H F; Olkoski, Denise; Vilperte, Vinicius; Zucchi, Maria I; Nodari, Rubens O

2014-06-01

Microsatellite primers were identified and characterized in Acca sellowiana in order to expand the limited number of pre-existing polymorphic markers for use in population genetic studies for conservation, phylogeography, breeding, and domestication. • A total of 10 polymorphic microsatellite primers were designed from clones obtained from a simple sequence repeat (SSR)-enriched genomic library. The primers amplified di- and trinucleotide repeats with four to 27 alleles per locus. In all tested populations, the observed heterozygosity ranged from 0.269 to 1.0. • These new polymorphic SSR markers will allow future genetic studies to be denser, either for genetic structure characterization of natural populations or for studies involving genetic breeding and domestication process in A. sellowiana.

First Insights into the Genetic Diversity of the Pinewood Nematode in Its Native Area Using New Polymorphic Microsatellite Loci

PubMed Central

Mallez, Sophie; Castagnone, Chantal; Espada, Margarida; Vieira, Paulo; Eisenback, Jonathan D.; Mota, Manuel; Guillemaud, Thomas; Castagnone-Sereno, Philippe

2013-01-01

The pinewood nematode, Bursaphelenchus xylophilus, native to North America, is the causative agent of pine wilt disease and among the most important invasive forest pests in the East-Asian countries, such as Japan and China. Since 1999, it has been found in Europe in the Iberian Peninsula, where it also causes significant damage. In a previous study, 94 pairs of microsatellite primers have been identified in silico in the pinewood nematode genome. In the present study, specific PCR amplifications and polymorphism tests to validate these loci were performed and 17 microsatellite loci that were suitable for routine analysis of B. xylophilus genetic diversity were selected. The polymorphism of these markers was evaluated on nematodes from four field origins and one laboratory collection strain, all originate from the native area. The number of alleles and the expected heterozygosity varied between 2 and 11 and between 0.039 and 0.777, respectively. First insights into the population genetic structure of B. xylophilus were obtained using clustering and multivariate methods on the genotypes obtained from the field samples. The results showed that the pinewood nematode genetic diversity is spatially structured at the scale of the pine tree and probably at larger scales. The role of dispersal by the insect vector versus human activities in shaping this structure is discussed. PMID:23554990

Microsatellite polymorphisms associated with human behavioural and psychological phenotypes including a gene-environment interaction.

PubMed

Bagshaw, Andrew T M; Horwood, L John; Fergusson, David M; Gemmell, Neil J; Kennedy, Martin A

2017-02-03

The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies. We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance. The repeats were a highly conserved poly-AC microsatellite in the upstream promoter region of the T-box brain 1 (TBR1) gene and three previously studied STRs in the activating enhancer-binding protein 2-beta (AP2-β) and androgen receptor (AR) genes. Where significance was found we used multiple regression to assess the influence of confounding factors. Carriers of the shorter, most common, allele of the AR gene's GGN microsatellite polymorphism had fewer anxiety-related symptoms, which was consistent with previous studies, but in our study this was not significant following Bonferroni correction. No associations with two repeats in the AP2-β gene withstood this correction. A novel finding was that carriers of the minor allele of the TBR1 AC microsatellite were at higher risk of conduct problems in childhood at age 7-9 (p = 0.0007, which did pass Bonferroni correction). Including maternal smoking during pregnancy (MSDP) in models controlling for potentially confounding influences showed that an interaction between TBR1 genotype and MSDP was a significant predictor of conduct problems in childhood and adolescence (p < 0.001), and of self-reported criminal behaviour up to age 25 years (p ≤ 0.02). This interaction remained significant after controlling for possible confounders including maternal age at birth, socio-economic status and education, and offspring birth weight. The potential functional importance

Isolation and cross-familial amplification of 41 microsatellites for the brook charr (Salvelinus fontinalis)

USGS Publications Warehouse

Perry, G.M.L.; King, T.L.; St. -Cyr, J.; Valcourt, M.; Bernatchez, L.

2005-01-01

The brook charr (Salvelinus fontinalis; Osteichthyes: Salmonidae) is a phenotypically diverse fish species inhabiting much of North America. But relatively few genetic diagnostic resources are available for this fish species. We isolated 41 microsatellites from S. fontinalis polymorphic in one or more species of salmonid fish. Thirty-seven were polymorphic in brook charr, 15 in the congener Arctic charr (Salvelinus alpinus) and 14 in the lake charr (Salvelinus namaycush). Polymorphism was also relatively high in Oncorhynchus, where 21 loci were polymorphic in rainbow trout (Oncorhynchus mykiss) and 16 in cutthroat trout (Oncorhynchus clarkii) but only seven and four microsatellite loci were polymorphic in the more distantly related lake whitefish (Coregonus clupeaformis) and Atlantic salmon (Salmo salar), respectively. One duplicated locus (Sfo228Lav) was polymorphic at both duplicates in S. fontinalis. ?? 2005 Blackwell Publishing Ltd.

The ploidy races of Atriplex confertifolia (chenopodiaceae)

Treesearch

Stewart C. Sanderson

2011-01-01

Previous accounts of polyploidy in the North American salt desert shrub Atriplex confertifolia (shadscale) have dealt with the distribution of polyploidy and the morphological and secondary chemical differences between races. The present study amplifies these studies and reveals additional ploidy-flavonoid races, with ploidy levels known to extend from 2x to 12x, and...

Isolation and characterization of 30 microsatellite loci for Cunninghamia lanceolata (Taxodiaceae)1

PubMed Central

Wang, Si-Si; Zhang, Yang; Liu, De-Chen; Sun, Xiao-Wei; Wang, Rong; Li, Yuan-Yuan

2017-01-01

Premise of the study: To quantify the population-level genetic characteristics of Cunninghamia lanceolata (Taxodiaceae), an important timber conifer, we developed 30 pairs of microsatellite primers based on the nuclear genome. Methods and Results: Using the streptavidin-biotin capture system, we developed 14 polymorphic and 16 monomorphic microsatellites. Polymorphisms were detected in 14 loci using 94 individual trees that were collected from three C. lanceolata populations in Hubei and Zhejiang provinces and in Chongqing Municipality, China. There were three to 30 alleles per locus, and the observed and expected heterozygosities ranged from 0.0313–0.8333 and from 0.0313–0.9246, respectively. Cross-species amplification showed that two to seven polymorphic loci were functional in three of the five related species that were collected. Conclusions: Our newly developed microsatellite primers provide neutral molecular markers that are beneficial to future studies of population genetics and germplasm conservation of C. lanceolata. PMID:28989826

Population Genetics of Verticillium dahliae in Iran Based on Microsatellite and Single Nucleotide Polymorphism Markers.

PubMed

Rafiei, Vahideh; Banihashemi, Ziaeddin; Bautista-Jalon, Laura S; Del Mar Jiménez-Gasco, Maria; Turgeon, B Gillian; Milgroom, Michael G

2018-06-01

Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, single nucleotide polymorphisms (SNPs), and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, respectively, all but four isolates were assigned to lineage 2B 824 ; four isolates were assigned to lineage 4B. The inferred coalescent genealogy of isolates in lineage 2B 824 showed a clear divergence into two clades that corresponded to geographic origin and host. Haplotypes of cotton and pistachio isolates sampled from central Iran were in one clade, and those of isolates from Prunus spp. sampled from northwestern Iran were in the other. The strong divergence in haplotypes between the two clades suggests that there were at least two separate introductions of lineage 2B 824 to different parts of Iran. Given the history of cotton and pistachio cultivation and Verticillium wilt in Iran, these results are consistent with the hypothesis that cotton was historically a likely source inoculum causing Verticillium wilt in pistachio.

Three novel polymorphic microsatellite markers for the glaucoma locus GLC1B by datamining tetranucleotide repeats on chromosome 2p12-q12

PubMed Central

2009-01-01

In order to identify new markers around the glaucoma locus GLC1B as a tool to refine its critical region at 2p11.2-2q11.2, we searched the critical region sequence obtained from the UCSC database for tetranucleotide (GATA)n and (GTCT)n repeats of at least 10 units in length. Three out of four potential microsatellite loci were found to be polymorphic, heterozygosity ranging from 64.56% to 79.59%. The identified markers are useful not only for GLC1B locus but also for the study of other disease loci at 2p11.2-2q11.2, a region with scarcity of microsatellite markers. PMID:21637444

Microsatellite markers for Plathymenia reticulata (Leguminosae)1.

PubMed

Oliveira, Fernanda A; Tarazi, Roberto; Menezes, Ivandilson P P; Van Den Berg, Cassio; Tsai, Siu M; Gaiotto, Fernanda A

2012-10-01

Microsatellite markers were developed and characterized to investigate genetic diversity and gene flow and to help in conservation efforts for the endangered timber species Plathymenia reticulata. • Eleven microsatellite loci were characterized using 60 adult trees of two populations of P. reticulata from the Atlantic Forest of southern Bahia, Brazil. Of these, nine loci were polymorphic, with an average of 4.39 alleles per locus. The average expected heterozygosity per population ranged from 0.47 to 0.55. The combined exclusion probability was 0.99996. • Our results reveal that the microsatellite markers developed in this study are an effective tool for paternity and genetic structure analysis that may be useful for conservation strategies.

Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

PubMed

Much, Melissa; Buza, Natalia; Hui, Pei

2014-03-01

Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences. Copyright © 2014 Elsevier Inc. All rights reserved.

Isolation and characterization of 12 microsatellite loci in soapbark, Quillaja saponaria (Quillajaceae)1

PubMed Central

Letelier, Luis; Harvey, Nick; Valderrama, Aly; Stoll, Alexandra; González-Rodríguez, Antonio

2015-01-01

Premise of the study: Microsatellite primers were developed for the endemic Chilean tree Quillaja saponaria (Quillajaceae), a common member of the sclerophyllous Mediterranean forest, to investigate intraspecific patterns of genetic diversity and structure. Methods and Results: Using an enriched library, 12 polymorphic microsatellite loci were developed in Q. saponaria. All loci consisted of dinucleotide repeats. The average number of alleles per locus was 5.3 (2–13), with a total of 64 alleles recorded in 39 individuals from three populations. Conclusions: The microsatellite markers described here are the first characterized for Q. saponaria. The polymorphic loci will be useful in studies of genetic diversity and genetic population differentiation in natural populations of this species. PMID:25995980

Exploring single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes in the jellyfish (Rhopilema esculentum) by transcriptome sequencing.

PubMed

Li, Yunfeng; Zhou, Zunchun; Tian, Meilin; Tian, Yi; Dong, Ying; Li, Shilei; Liu, Weidong; He, Chongbo

2017-08-01

In this study, single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes (DEGs) in the oral parts, gonads, and umbrella parts of the jellyfish Rhopilema esculentum were analyzed by RNA-Seq technology. A total of 76.4 million raw reads and 72.1 million clean reads were generated from deep sequencing. Approximately 119,874 tentative unigenes and 149,239 transcripts were obtained. A total of 1,034,708 SNP markers were detected in the three tissues. For microsatellite mining, 5088 SSRs were identified from the unigene sequences. The most frequent repeat motifs were mononucleotide repeats, which accounted for 61.93%. Transcriptome comparison of the three tissues yielded a total of 8841 DEGs, of which 3560 were up-regulated and 5281 were down-regulated. This study represents the greatest sequencing effort carried out for a jellyfish and provides the first high-throughput transcriptomic resource for jellyfish. Copyright © 2017 Elsevier B.V. All rights reserved.

Isolation and Characterization of Eleven Polymorphic Microsatellite Loci for the Valuable Medicinal Plant Dendrobium huoshanense and Cross-Species Amplification

PubMed Central

Wang, Hui; Chen, Nai-Fu; Zheng, Ji-Yang; Wang, Wen-Cai; Pei, Yun-Yun; Zhu, Guo-Ping

2012-01-01

Dendrobium huoshanense (Orchidaceae) is a perennial herb and a widely used medicinal plant in Traditional Chinese medicine (TCM) endemic to Huoshan County town in Anhui province in Southeast China. A microsatellite-enriched genomic DNA library of D. huoshanense was developed and screened to identify marker loci. Eleven polymorphic loci were isolated and analyzed by screening 25 individuals collected from a natural population. The number of alleles per locus ranged from 2 to 5. The observed and expected heterozygosities ranged from 0.227 to 0.818 and from 0.317 to 0.757, respectively. Two loci showed significant deviations from Hardy-Weinberg equilibrium and four of the pairwise comparisons of loci revealed linkage disequilibrium (p < 0.05). These microsatellite loci were cross-amplified for five congeneric species and seven loci can be amplified in all species. These simple sequence repeats (SSR) markers are useful in genetic studies of D. huoshanense and other related species and in conservation decision-making. PMID:23222682

Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

PubMed

Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

2015-01-01

Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae)

PubMed Central

Bonatelli, Isabel A. S.; Carstens, Bryan C.; Moraes, Evandro M.

2015-01-01

Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms. PMID:26561396

Microsatellite marker analysis of the genetic variability in Hanoverian Hounds.

PubMed

Lüpke, L; Distl, O

2005-04-01

Genetic variability of the dog breed Hanoverian Hound was analysed using a set of 16 microsatellites. The sample of 92 dogs was representative for the total current population [n=334, inbreeding coefficient 9.2%, relationship coefficient 11.2%] with respect to the level and distribution of the inbreeding and relationship coefficients. All microsatellites used were in Hardy-Weinberg equilibrium. The average number of alleles was 6.4. The average observed heterozygosity (H(O)) was slightly higher than the expected heterozygosity (H(E)). Dinucleotide microsatellites exhibited lower polymorphism information content (PIC) than tetranucleotide microsatellites (0.52 versus 0.66). The average PIC was 0.61. The individual inbreeding coefficient was negatively related to the average H(O) of all microsatellites, whereas the proportion of genes from introducing of Hanoverian Hounds from abroad showed no relationships to H(O). We found that the genetic variability in the Hanoverian Hounds analysed here was unexpectedly higher than that previously published for dog breeds of similar population size. Even in dog breeds of larger population size heterogyzosity was seldom higher than that observed here. The rather high genetic variability as quantified by polymorphic microsatellites in Hanoverian Hounds may be due to a large genetic variation in the founder animals of this breed and to the fact that this genetic diversity could be maintained despite genetic bottlenecks experienced by this breed in the 1920s and 1950s and despite the presence of high inbreeding and relationship coefficients for more than 50 years.

Heterogeneity, histological features and DNA ploidy in oral carcinoma by image-based analysis.

PubMed

Diwakar, N; Sperandio, M; Sherriff, M; Brown, A; Odell, E W

2005-04-01

Oral squamous carcinomas appear heterogeneous on DNA ploidy analysis. However, this may be partly a result of sample dilution or the detection limit of techniques. The aim of this study was to determine whether oral squamous carcinomas are heterogeneous for ploidy status using image-based ploidy analysis and to determine whether ploidy status correlates with histological parameters. Multiple samples from 42 oral squamous carcinomas were analysed for DNA ploidy using an image-based system and scored for histological parameters. 22 were uniformly aneuploid, 1 uniformly tetraploid and 3 uniformly diploid. 16 appeared heterogeneous but only 8 appeared to be genuinely heterogeneous when minor ploidy histogram peaks were taken into account. Ploidy was closely related to nuclear pleomorphism but not differentiation. Sample variation, detection limits and diagnostic criteria account for much of the ploidy heterogeneity observed. Confident diagnosis of diploid status in an oral squamous cell carcinoma requires a minimum of 5 samples.

Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

PubMed Central

Pajuelo, Mónica J.; Eguiluz, María; Dahlstrom, Eric; Requena, David; Guzmán, Frank; Ramirez, Manuel; Sheen, Patricia; Frace, Michael; Sammons, Scott; Cama, Vitaliano; Anzick, Sarah; Bruno, Dan; Mahanty, Siddhartha; Wilkins, Patricia; Nash, Theodore; Gonzalez, Armando; García, Héctor H.; Gilman, Robert H.; Porcella, Steve; Zimic, Mirko

2015-01-01

Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. Methods For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. Results The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. Conclusions/Significance The availability of draft

Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium.

PubMed

Pajuelo, Mónica J; Eguiluz, María; Dahlstrom, Eric; Requena, David; Guzmán, Frank; Ramirez, Manuel; Sheen, Patricia; Frace, Michael; Sammons, Scott; Cama, Vitaliano; Anzick, Sarah; Bruno, Dan; Mahanty, Siddhartha; Wilkins, Patricia; Nash, Theodore; Gonzalez, Armando; García, Héctor H; Gilman, Robert H; Porcella, Steve; Zimic, Mirko

2015-12-01

Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. The availability of draft genomes for T. solium represents a significant step

Identification and characterization of microsatellite markers from the tropical sea cucumber, Stichopus horrens (Selenka).

PubMed

Shangguan, J B; Li, Z B; Yuan, Y; Huang, Y S

2015-10-28

Tropical commercial sea cucumber Stichopus horrens is extensively distributed throughout the tropical Indo-Pacific region, and wild stocks have been severely depleted over the past decade. In this study, we used the microsatellite enrichment library of S. horrens to identify and characterize 13 microsatellite loci, including 11 polymorphic loci and 2 monomorphic loci. Among the 11 polymorphic loci, the number of alleles was 3-8. The observed and expected heterozygosity varied from 0.1364 to 0.8966 and from 0.1653 to 0.7551, respectively. Additionally, all 11 polymorphic loci showed moderate and high polymorphism with the polymorphism information content (0.271-0.7311). A total of 9 polymorphic loci were in Hardy-Weinberg equilibrium, except for 2 loci (adjusted P = 0.004545). Linkage disequilibrium was not detected in any pairs of polymorphic loci. The present study will be useful for studying genetic structure, population conservation, and breeding of wild S. horrens; moreover, our results contribute to the phylogeny and evolutionary research of Holothuroidea.

Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus).

PubMed

Bertolotti, Alicia C; Griffiths, Sarah M; Truelove, Nathan K; Box, Stephen J; Preziosi, Richard F; Salinas de Leon, Pelayo

2015-01-01

The white-spotted sandbass (Paralabrax albomaculatus) is a commercially important species in the Galapagos Marine Reserve, but is classified as endangered in the IUCN Red List. For this study, 10 microsatellite loci were isolated and characterized using Illumina paired-end sequencing. These loci can be used for genetic studies of population structure and connectivity to aid in the management of the white-spotted sandbass and other closely-related species. The 10 characterized loci were polymorphic, with 11-49 alleles per locus, and observed heterozygosity ranged from 0.575 to 0.964. This set of markers is the first to be developed for this species.

Isolation and characterization of novel microsatellite markers from the sika deer (Cervus nippon) genome.

PubMed

Li, Y M; Bai, C Y; Niu, W P; Yu, H; Yang, R J; Yan, S Q; Zhang, J Y; Zhang, M J; Zhao, Z H

2015-09-28

Microsatellite markers are widely and evenly distributed, and are highly polymorphic. Rapid and convenient detection through automated analysis means that microsatellite markers are widely used in the construction of plant and animal genetic maps, in quantitative trait loci localization, marker-assisted selection, identification of genetic relationships, and genetic diversity and phylogenetic tree construction. However, few microsatellite markers remain to be isolated. We used streptavidin magnetic beads to affinity-capture and construct a (CA)n microsatellite DNA-enriched library from sika deer. We selected sequences containing more than six repeats to design primers. Clear bands were selected, which were amplified using non-specific primers following PCR amplification to screen polymorphisms in a group of 65 unrelated sika deer. The positive clone rate reached 82.9% by constructing the enriched library, and we then selected positive clones for sequencing. There were 395 sequences with CA repeats, and the CA repeat number was 4-105. We selected sequences containing more than six repeats to design primers, of which 297 pairs were designed. We next selected clear bands and used non-specific primers to amplify following PCR amplification. In total, 245 pairs of primers were screened. We then selected 50 pairs of primers to randomly screen for polymorphisms. We detected 47 polymorphic and 3 monomorphic loci in 65 unrelated sika deer. These newly isolated and characterized microsatellite loci can be used to construct genetic maps and for lineage testing in deer. In addition, they can be used for comparative genomics between Cervidae species.

Microsatellite primers for the endangered aquatic herb, Ottelia acuminata (Hydrocharitaceae).

PubMed

Xu, Chao; Du, Zhi-Yuan; Chen, Jin-Ming; Wang, Qing-Feng

2012-06-01

Microsatellite primers were developed in the endangered aquatic herb, Ottelia acuminata, to characterize its genetic diversity and understand its population structure. Eight polymorphic microsatellite markers were developed from two populations of O. acuminata in China. The number of alleles per locus ranged from one to 15; the observed and expected heterozygosities ranged from 0 to 0.885 and from 0 to 0.888, respectively, in the two populations. Selected loci also amplified successfully in O. sinensis. These microsatellite markers will facilitate further studies on the conservation genetics and evolutionary history of O. acuminata.

Isolation and characterization of microsatellite markers of sea cucumber Stichopus horrens.

PubMed

Li, Z B; Dai, G; Shangguan, J B; Ning, Y F; Li, Y Y; Chen, R B; Yuan, Y; Huang, Y S

2015-07-28

Curry fish (Stichopus horrens) is a tropical holothurian species and is widely distributed in the India-West Pacific. In the present study, 9 polymorphic microsatellite loci were isolated and characterized for S. horrens. These loci were tested in 30 individuals from Hainan Island in China. The number of alleles ranged from 2 to 5. The polymorphism information content ranged from 0.348-0.584. The levels of observed and expected heterozygosities varied from 0.1500-0.8000 and from 0.2014-0.5000, respectively. Most loci were in Hardy-Weinberg equilibrium, except HCS1-27 and HCS2-7, after sequential Bonferroni's correction, and no significant linkage disequilibrium was detected for any pairwise combination of loci. These polymorphic microsatellite loci will be useful for studying population structure and conservation strategy design for S. horrens.

WebSat--a web software for microsatellite marker development.

PubMed

Martins, Wellington Santos; Lucas, Divino César Soares; Neves, Kelligton Fabricio de Souza; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. The web tool may be accessed at http://purl.oclc.org/NET/websat/

Microsatellite loci development in mycoheterotrophic Corallorhiza maculata with amplification in C. mertensiana

Treesearch

Sarah E. Hopkins; D. Lee Taylor

2011-01-01

Microsatellite primers were developed for the first time in the species Corallorhiza maculata, a nonphotosynthetic orchid that is becoming a model for studying mycorrhizal specificity. Eight polymorphic microsatellite markers were developed using an enrichment and cloning protocol. The number of alleles for each locus ranged from two to seven. The...

Invasion genetics of the Bermuda buttercup (Oxalis pes-caprae): complex intercontinental patterns of genetic diversity, polyploidy and heterostyly characterize both native and introduced populations.

PubMed

Ferrero, Victoria; Barrett, Spencer C H; Castro, Sílvia; Caldeirinha, Patrícia; Navarro, Luis; Loureiro, João; Rodríguez-Echeverría, Susana

2015-05-01

Genetic diversity in populations of invasive species is influenced by a variety of factors including reproductive systems, ploidy level, stochastic forces associated with colonization and multiple introductions followed by admixture. Here, we compare genetic variation in native and introduced populations of the clonal plant Oxalis pes-caprae to investigate the influence of reproductive mode and ploidy on levels of diversity. This species is a tristylous geophyte native to South Africa. Invasive populations throughout much of the introduced range are composed of a sterile clonal pentaploid short-styled form. We examined morph ratios, ploidy level, reproductive mode and genetic diversity at nuclear microsatellite loci in 10 and 12 populations from South Africa and the Western Mediterranean region, respectively. Flow cytometry confirmed earlier reports of diploids and tetraploids in the native range, with a single population containing pentaploid individuals. Introduced populations were composed mainly of pentaploids, but sexual tetraploids were also found. There was clear genetic differentiation between ploidy levels, but sexual populations from both regions were not significantly different in levels of diversity. Invasive populations of the pentaploid exhibited dramatically reduced levels of diversity but were not genetically uniform. The occurrence of mixed ploidy levels and stylar polymorphism in the introduced range is consistent with multiple introductions to the Western Mediterranean. This inference was supported by variation patterns at microsatellite loci. Our study indicates that some invasive populations of Oxalis pes-caprae are not entirely clonal, as often assumed, and multiple introductions and recombination have the potential to increase genetic variation in the introduced range. © 2014 John Wiley & Sons Ltd.

Isolation of novel microsatellite markers and their application for genetic diversity and parentage analyses in sika deer.

PubMed

Yang, Wanyun; Zheng, Junjun; Jia, Boyin; Wei, Haijun; Wang, Guiwu; Yang, Fuhe

2018-02-15

Every part of the sika deer (Cervus nippon) body is valuable traditional Chinese medicine. And sika deer is the most important semi-domestic medicinal animal that is widely bred in Jilin province northeast of China. But few studies had been conducted to characterize the microsatellite markers derived from sika deer. We firstly used IlluminaHiSeq™2500 sequencing technology obtained 125Mbp genomic data of sika deer. Using microsatellite identification tool (MISA), 22,479 microsatellites were identified. From these data, 100 potential primers were selected for further polymorphic validation, finally, 76 primer pairs were successfully amplified and 29 primer pairs were found to be obvious polymorphic in 8 different individuals. Using those polymorphic microsatellite markers, we analyzed the genetic diversity of Jilin sika deer population. The mean number of alleles of the 29 loci is 9.31 based on genotyping blood DNA from 96 Jilin sika deer; The mean expected heterozygosity and polymorphic information content (PIC) value of the 29 loci is 0.72 and 0.68 respectively, and among which 26 loci are highly polymorphic (PIC>0.50). According to the electrophoretic results and PIC value of these 29 loci, 10 loci with combined paternity exclusion probabilities>99.99% were selected to use in parentage verification for 16 sika deer. All the offspring of a family could be successfully assigned to their biological father. These microsatellite markers generated in this study could greatly facilitate future studies of molecular breeding in sika deer. Copyright © 2017 Elsevier B.V. All rights reserved.

Microsatellite markers for Leucobryum boninense (Leucobryaceae), endemic to the Bonin Islands, Japan.

PubMed

Oguri, Emiko; Yamaguchi, Tomio; Kajita, Tadashi; Murakami, Noriaki

2013-05-01

Microsatellite primers were developed for Leucobryum boninense, endemic to the Bonin Islands, Japan, to investigate its level of genetic diversity and population genetic structure. • Using next-generation sequencing, 21 primer sets were developed, among which nine loci were polymorphic in the populations of the Bonin Islands. Among these polymorphic loci, the number of alleles per locus ranged from two to 10 (mean = 3.444) and the expected heterozygosity ranged from 0.066 to 0.801 (mean = 0.338). • These results indicate the utility of the nine microsatellite markers that we developed for population genetic studies of L. boninense.

Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

USGS Publications Warehouse

Ramirez-Macias, D.; Shaw, K.; Ward, R.; Galvan-Magana, F.; Vazquez-Juarez, R.

2009-01-01

In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy–Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.

Genetic variation at microsatellite loci in the tropical herb Aphelandra aurantiaca (Acanthaceae).

PubMed

Suárez-Montes, Pilar; Tapia-López, Rosalinda; Núñez-Farfán, Juan

2015-11-01

To assess the effect of forest fragmentation on genetic variation and population structure of Aphelandra aurantiaca (Acanthaceae), a tropical and ornamental herbaceous perennial plant, we developed the first microsatellite primers for the species. Fourteen microsatellite markers were isolated and characterized from A. aurantiaca genomic libraries enriched for di-, tri-, and tetranucleotide repeat motifs. Polymorphism was evaluated in 107 individuals from four natural populations. Twelve out of 14 genetic markers were polymorphic. The number of alleles per locus ranged from two to 12, and the observed and expected heterozygosities ranged from 0.22 to 0.96 and from 0.20 to 0.87, respectively. Fixation indices ranged from -0.41 to 0.44. These newly developed microsatellite markers for A. aurantiaca will be useful for future population genetic studies, specifically to detect the possible loss of genetic diversity due to habitat fragmentation.

Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek).

PubMed

Shrivastava, Divya; Verma, Priyanka; Bhatia, Sabhyata

2014-09-01

Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard's similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.

Characterization of 10 new nuclear microsatellite markers in Acca sellowiana (Myrtaceae)1

PubMed Central

Klabunde, Gustavo H. F.; Olkoski, Denise; Vilperte, Vinicius; Zucchi, Maria I.; Nodari, Rubens O.

2014-01-01

• Premise of the study: Microsatellite primers were identified and characterized in Acca sellowiana in order to expand the limited number of pre-existing polymorphic markers for use in population genetic studies for conservation, phylogeography, breeding, and domestication. • Methods and Results: A total of 10 polymorphic microsatellite primers were designed from clones obtained from a simple sequence repeat (SSR)–enriched genomic library. The primers amplified di- and trinucleotide repeats with four to 27 alleles per locus. In all tested populations, the observed heterozygosity ranged from 0.269 to 1.0. • Conclusions: These new polymorphic SSR markers will allow future genetic studies to be denser, either for genetic structure characterization of natural populations or for studies involving genetic breeding and domestication process in A. sellowiana. PMID:25202632

Development of 10 highly-polymorphic microsatellite markers in the vulnerable Galápagos land iguanas (genus Conolophus).

PubMed

Rosa, Sabrina F P; Monteyne, Daniel; Milinkovitch, Michel C

2009-01-01

The two species of Galápagos land iguanas (Conolophus subcristatus and C. pallidus) are listed as 'vulnerable' species by the International Union for the Conservation of Nature (IUCN Red List; http://www.iucnredlist.org). Here, we report on the isolation and characterization of 10 microsatellite markers using 562 individuals sampled on all Galápagos islands where Conolophus species occur today. We show that these 10 loci are highly polymorphic and display diagnostic alleles for five out of the six island populations. These markers will be useful for Conolophus population genetic analyses as well as for guiding ongoing captive breeding programmes. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Isolation and characterization of polymorphic microsatellite markers in the black spiny tailed iguana (Ctenosaura pectinata) and their cross-utility in other Ctenosaura.

PubMed

Zarza, Eugenia; Pereyra, Ricardo T; Reynoso, Victor H; Emerson, Brent C

2009-01-01

We isolated and characterized 10 polymorphic microsatellite loci from the Mexican black iguana (Ctenosaura pectinata) and assessed levels of polymorphism in sampling sites located in the northern areas of the species' distribution range. Two to 19 alleles per locus and observed heterozygosity ranging from 0.15 to 0.96 were detected. These markers will be useful to describe population genetic structure, the extent of gene flow in contact zones, to study the mating system of the species and to address conservation genetics issues. Additionally, we evaluated the potential utility of these markers for studies of other species within the genus Ctenosaura (i.e. C. hemilopha, C. similis and C. oaxacana). © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

WebSat ‐ A web software for microsatellite marker development

PubMed Central

Martins, Wellington Santos; Soares Lucas, Divino César; de Souza Neves, Kelligton Fabricio; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. Availability The web tool may be accessed at http://purl.oclc.org/NET/websat/ PMID:19255650

Microsatellite diversity of isolates of the parasitic nematode Haemonchus contortus.

PubMed

Otsen, M; Plas, M E; Lenstra, J A; Roos, M H; Hoekstra, R

2000-09-01

The alarming development of anthelmintic resistance in important gastrointestinal nematode parasites of man and live-stock is caused by selection for specific genotypes. In order to provide genetic tools to study the nematode populations and the consequences of anthelmintic treatment, we isolated and sequenced 59 microsatellites of the sheep and goat parasite Haemonchus contortus. These microsatellites consist typically of 2-10 tandems CA/GT repeats that are interrupted by sequences of 1-10 bp. A predominant cause of the imperfect structure of the microsatellites appeared mutations of G/C bp in the tandem repeat. About 44% of the microsatellites were associated with the HcREP1 direct repeat, and it was demonstrated that a generic HcREP1 primer could be used to amplify HcREP1-associated microsatellites. Thirty microsatellites could be typed by polymerase chain reaction (PCR) of which 27 were polymorphic. A number of these markers were used to detect genetic contamination of an experimental inbred population. The microsatellites may also contribute to the genetic mapping of drug resistance genes.

Ancient Evolutionary Trade-Offs between Yeast Ploidy States

PubMed Central

Zörgö, Enikö; Chwialkowska, Karolina; Gjuvsland, Arne B.; Garré, Elena; Sunnerhagen, Per; Liti, Gianni; Blomberg, Anders; Omholt, Stig W.; Warringer, Jonas

2013-01-01

The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life. Here, we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths of their natural genotypic and phenotypic space. Surprisingly, environment-specific influences of ploidy on reproduction were found to be the rule rather than the exception. These ploidy–environment interactions were well conserved across the 2 billion generations separating the two species, suggesting that they are the products of strong selection. Previous hypotheses of generalizable advantages of haploidy or diploidy in ecological contexts imposing nutrient restriction, toxin exposure, and elevated mutational loads were rejected in favor of more fine-grained models of the interplay between ecology and ploidy. On a molecular level, cell size and mating type locus composition had equal, but limited, explanatory power, each explaining 12.5%–17% of ploidy–environment interactions. The mechanism of the cell size–based superior reproductive efficiency of haploids during Li+ exposure was traced to the Li+ exporter ENA. Removal of the Ena transporters, forcing dependence on the Nha1 extrusion system, completely altered the effects of ploidy on Li+ tolerance and evoked a strong diploid superiority, demonstrating how genetic variation at a single locus can completely reverse the relative merits of haploidy and diploidy. Taken together, our findings unmasked a dynamic interplay between ploidy and ecology that was of unpredicted evolutionary importance and had multiple molecular roots. PMID:23555297

[Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism].

PubMed

Zelenina, D A; Khrustaleva, A M; Volkov, A A

2006-05-01

Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94-100%) were somewhat higher than those based on microsatellite data (74-84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.

Development and characterization of 16 polymorphic microsatellite loci for the Alaska blackfish (Esociformes: Dallia pectoralis)

USGS Publications Warehouse

Campbell, Matthew A.; Sage, George K.; DeWilde, Rachel L.; López, J. Andres; Talbot, Sandra L.

2014-01-01

Blackfishes (Esociformes: Esocidae: Dallia), small fishes with relictual distributions, are unique in being the only primary freshwater fish genus endemic to Beringia. Although the number of species of Dallia is debated, disjunct populations and distinct mitochondrial divisions that predate the end of the last glacial maximum are apparent. We developed sixteen polymorphic microsatellites from the Alaska blackfish (Dallia pectoralis) to study genetic diversity in Dallia. Genotypes from two populations, Denali (n = 31) and Bethel (n = 35), demonstrated the usefulness of the loci for population-level investigation. Observed and expected heterozygosity averaged 18.6 and 19.8 % in Denali and 61.1 and 63.7 % in Bethel. Number of alleles at each locus averaged 3.50 in Denali and 9.63 in Bethel. The observed signature of variability and structuring between populations is consistent with mitochondrial data.

Isolation and characterization of microsatellite markers from the great hornbill, Buceros bicornis.

PubMed

Chamutpong, Siriphatr; Saito, Daichi S; Viseshakul, Nareerat; Nishiumi, Isao; Poonswad, Pilai; Ponglikitmongkol, Mathurose

2009-03-01

Thirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean polymorphic information content was 0.62. Among these, three loci deviated from the Hardy-Weinberg equilibrium. However, no significant genotypic disequilibrium was detected between any pair of loci. These microsatellite markers are useful for the population genetic study of the great hornbill. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Clinical application of DNA ploidy to cervical cancer screening: A review.

PubMed

Garner, David

2014-12-10

Screening for cervical cancer with DNA ploidy assessment by automated quantitative image cytometry has spread throughout China over the past decade and now an estimated 1 million tests per year are done there. Compared to conventional liquid based cytology, DNA ploidy has competitive accuracy with much higher throughput per technician. DNA ploidy has the enormous advantage that it is an objective technology that can be taught in typically 2 or 3 wk, unlike qualitative cytology, and so it can enable screening in places that lack sufficient qualified cytotechnologists and cytopathologists for conventional cytology. Most papers on experience with application of the technology to cervical cancer screening over the past decade were published in the Chinese language. This review aims to provide a consistent framework for analysis of screening data and to summarize some of the work published from 2005 to the end of 2013. Of particular interest are a few studies comparing DNA ploidy with testing for high risk human papilloma virus (hrHPV) which suggest that DNA ploidy is at least equivalent, easier and less expensive than hrHPV testing. There may also be patient management benefits to combining hrHPV testing with DNA ploidy. Some knowledge gaps are identified and some suggestions are made for future research directions.

Clinical application of DNA ploidy to cervical cancer screening: A review

PubMed Central

Garner, David

2014-01-01

Screening for cervical cancer with DNA ploidy assessment by automated quantitative image cytometry has spread throughout China over the past decade and now an estimated 1 million tests per year are done there. Compared to conventional liquid based cytology, DNA ploidy has competitive accuracy with much higher throughput per technician. DNA ploidy has the enormous advantage that it is an objective technology that can be taught in typically 2 or 3 wk, unlike qualitative cytology, and so it can enable screening in places that lack sufficient qualified cytotechnologists and cytopathologists for conventional cytology. Most papers on experience with application of the technology to cervical cancer screening over the past decade were published in the Chinese language. This review aims to provide a consistent framework for analysis of screening data and to summarize some of the work published from 2005 to the end of 2013. Of particular interest are a few studies comparing DNA ploidy with testing for high risk human papilloma virus (hrHPV) which suggest that DNA ploidy is at least equivalent, easier and less expensive than hrHPV testing. There may also be patient management benefits to combining hrHPV testing with DNA ploidy. Some knowledge gaps are identified and some suggestions are made for future research directions. PMID:25493231

Characterization of 42 microsatellite markers from poison ivy, Toxicodendron radicans (Anacardiaceae).

PubMed

Hsu, Tsai-Wen; Shih, Huei-Chuan; Kuo, Chia-Chi; Chiang, Tzen-Yuh; Chiang, Yu-Chung

2013-10-14

Poison ivy, Toxicodendron radicans, and poison oaks, T. diversilobum and T. pubescens, are perennial woody species of the Anacardiaceae and are poisonous, containing strong allergens named urushiols that cause allergic contact dermatitis. Poison ivy is a species distributed from North America to East Asia, while T. diversilobum and T. pubescens are distributed in western and eastern North America, respectively. Phylogreography and population structure of these species remain unclear. Here, we developed microsatellite markers, via constructing a magnetic enriched microsatellite library, from poison ivy. We designed 51 primer pairs, 42 of which successfully yielded products that were subsequently tested for polymorphism in poison oak, and three subspecies of poison ivy. Among the 42 loci, 38 are polymorphic, while 4 are monomorphic. The number of alleles and the expected heterozygosity ranged from 1 to 12 and from 0.10 to 0.87, respectively, in poison ivy, while varied from 2 to 8 and, from 0.26 to 0.83, respectively in poison oak. Genetic analysis revealed distinct differentiation between poison ivy and poison oak, whereas slight genetic differentiation was detected among three subspecies of poison ivy. These highly polymorphic microsatellite fingerprints enable biologists to explore the population genetics, phylogeography, and speciation in Toxicodendron.

Characterization of 42 Microsatellite Markers from Poison Ivy, Toxicodendron radicans (Anacardiaceae)

PubMed Central

Hsu, Tsai-Wen; Shih, Huei-Chuan; Kuo, Chia-Chi; Chiang, Tzen-Yuh; Chiang, Yu-Chung

2013-01-01

Poison ivy, Toxicodendron radicans, and poison oaks, T. diversilobum and T. pubescens, are perennial woody species of the Anacardiaceae and are poisonous, containing strong allergens named urushiols that cause allergic contact dermatitis. Poison ivy is a species distributed from North America to East Asia, while T. diversilobum and T. pubescens are distributed in western and eastern North America, respectively. Phylogreography and population structure of these species remain unclear. Here, we developed microsatellite markers, via constructing a magnetic enriched microsatellite library, from poison ivy. We designed 51 primer pairs, 42 of which successfully yielded products that were subsequently tested for polymorphism in poison oak, and three subspecies of poison ivy. Among the 42 loci, 38 are polymorphic, while 4 are monomorphic. The number of alleles and the expected heterozygosity ranged from 1 to 12 and from 0.10 to 0.87, respectively, in poison ivy, while varied from 2 to 8 and, from 0.26 to 0.83, respectively in poison oak. Genetic analysis revealed distinct differentiation between poison ivy and poison oak, whereas slight genetic differentiation was detected among three subspecies of poison ivy. These highly polymorphic microsatellite fingerprints enable biologists to explore the population genetics, phylogeography, and speciation in Toxicodendron. PMID:24129176

PERMANENT GENETIC RESOURCES: Eighteen new polymorphic microsatellite markers for the endangered Florida manatee, Trichechus manatus latirostris.

PubMed

Tringali, Michael D; Seyoum, Seifu; Carney, Susan L; Davis, Michelle C; Rodriguez-Lopez, Marta A; Reynolds Iii, John E; Haubold, Elsa

2008-03-01

Here we describe 18 polymorphic microsatellite loci for Trichechus manatus latirostris (Florida manatee), isolated using a polymerase chain reaction-based technique. The number of alleles at each locus ranged from two to four (mean = 2.5) in specimens from southwest (n = 58) and northeast (n = 58) Florida. Expected and observed heterozygosities ranged from 0.11 to 0.67 (mean = 0.35) and from 0.02 to 0.78 (mean = 0.34), respectively. Departures from Hardy-Weinberg equilibrium occurred at two loci. There was no evidence of genotypic disequilibrium for any pair of loci. For individual identification, mean random-mating and θ-corrected match probabilities were 9.36 × 10(-7) and 1.95 × 10(-6) , respectively. © 2007 The Authors.

Breed traceability of buffalo meat using microsatellite genotyping technique.

PubMed

Kannur, Bheemashankar H; Fairoze, Md Nadeem; Girish, P S; Karabasanavar, Nagappa; Rudresh, B H

2017-02-01

Although buffalo has emerged as a major meat producing animal in Asia, major research on breed traceability has so far been focused on cattle (beef). This research gap on buffalo breed traceability has impelled development and validation of buffalo breed traceability using a set of eight microsatellite (STR) markers in seven Indian buffalo breeds (Bhadawari, Jaffaarabadi, Murrah, Mehsana, Nagpuri, Pandharpuri and Surti). Probability of sharing same profile by two individuals at a specific locus was computed considering different STR numbers, allele pooling in breed and population. Match probabilities per breed were considered and six most polymorphic loci were genotyped. Out of eight microsatellite markers studied, markers CSSMO47, DRB3 and CSSM060 were found most polymorphic. Developed technique was validated with known and unknown, blood and meat samples; wherein, samples were genetically traced in 24 out of 25 samples tested. Results of this study showed potential applications of the methodology and encourage other researchers to address the problem of buffalo traceability so as to create a world-wide archive of breed specific genotypes. This work is the first report of breed traceability of buffalo meat utilizing microsatellite genotyping technique.

Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims).

PubMed

Araya, Susan; Martins, Alexandre M; Junqueira, Nilton T V; Costa, Ana Maria; Faleiro, Fábio G; Ferreira, Márcio E

2017-07-21

The Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. edulis, the most important commercial Passiflora species, are still incipient. In spite of many recognized applications of microsatellite markers in genetics and breeding, their availability for passion fruit research remains restricted. Microsatellite markers in P. edulis are usually limited in number, show reduced polymorphism, and are mostly based on compound or imperfect repeats. Furthermore, they are confined to only a few Passiflora species. We describe the use of NGS technology to partially assemble the P. edulis genome in order to develop hundreds of new microsatellite markers. A total of 14.11 Gbp of Illumina paired-end sequence reads were analyzed to detect simple sequence repeat sites in the sour passion fruit genome. A sample of 1300 contigs containing perfect repeat microsatellite sequences was selected for PCR primer development. Panels of di- and tri-nucleotide repeat markers were then tested in P. edulis germplasm accessions for validation. DNA polymorphism was detected in 74% of the markers (PIC = 0.16 to 0.77; number of alleles/locus = 2 to 7). A core panel of highly polymorphic markers (PIC = 0.46 to 0.77) was used to cross-amplify PCR products in 79 species of Passiflora (including P. edulis), belonging to four subgenera (Astrophea, Decaloba, Distephana and Passiflora). Approximately 71% of the marker/species combinations resulted in positive amplicons in all species tested. DNA polymorphism was detected in germplasm accessions of six closely related Passiflora species (P. edulis, P. alata, P. maliformis, P. nitida, P. quadrangularis and P. setacea) and the data used for accession discrimination and species assignment. A database of P. edulis DNA sequences obtained by NGS technology was examined to identify microsatellite repeats in

An integrated chromosome map of microsatellite markers and inversion breakpoints for an Asian malaria mosquito, Anopheles stephensi.

PubMed

Kamali, Maryam; Sharakhova, Maria V; Baricheva, Elina; Karagodin, Dmitrii; Tu, Zhijian; Sharakhov, Igor V

2011-01-01

Anopheles stephensi is one of the major vectors of malaria in the Middle East and Indo-Pakistan subcontinent. Understanding the population genetic structure of malaria mosquitoes is important for developing adequate and successful vector control strategies. Commonly used markers for inferring anopheline taxonomic and population status include microsatellites and chromosomal inversions. Knowledge about chromosomal locations of microsatellite markers with respect to polymorphic inversions could be useful for better understanding a genetic structure of natural populations. However, fragments with microsatellites used in population genetic studies are usually too short for successful labeling and hybridization with chromosomes. We designed new primers for amplification of microsatellite loci identified in the A. stephensi genome sequenced with next-generation technologies. Twelve microsatellites were mapped to polytene chromosomes from ovarian nurse cells of A. stephensi using fluorescent in situ hybridization. All microsatellites hybridized to unique locations on autosomes, and 7 of them localized to the largest arm 2R. Ten microsatellites were mapped inside the previously described polymorphic chromosomal inversions, including 4 loci located inside the widespread inversion 2Rb. We analyzed microsatellite-based population genetic data available for A. stephensi in light of our mapping results. This study demonstrates that the chromosomal position of microsatellites may affect estimates of population genetic parameters and highlights the importance of developing physical maps for nonmodel organisms.

Characterization of a Canine Tetranucleotide Microsatellite Marker Located in the First Intron of the Tumor Necrosis Factor Alpha Gene

PubMed Central

WATANABE, Masashi; TANAKA, Kazuaki; TAKIZAWA, Tatsuya; SEGAWA, Kazuhito; NEO, Sakurako; TSUCHIYA, Ryo; MURATA, Michiko; MURAKAMI, Masaru; HISASUE, Masaharu

2013-01-01

ABSTRACT A polymorphic tetranucleotide (GAAT)n microsatellite in the first intron of the canine tumor necrosis factor alpha (TNFA) gene was characterized in this study; 139 dogs were analyzed: 22 Beagles, 26 Chihuahuas, 20 Miniature Dachshunds, 24 Miniature Poodles, 22 Pembroke Welsh Corgis and 25 Shiba Inus. We detected the presence of the 4 alleles (GAAT)5, (GAAT)6, (GAAT)7 and (GAAT)8, including 9 of the 10 expected genotypes. The expected heterozygosity (He) and the polymorphic information content (PIC) value of this microsatellite locus varied from 0.389 to 0.749 and from 0.333 to 0.682, respectively, among the 6 breeds. The allelic frequency differed greatly among breeds, but this microsatellite marker was highly polymorphic and could be a useful marker for the canine TNFA gene. PMID:24042337

Characterization of a canine tetranucleotide microsatellite marker located in the first intron of the tumor necrosis factor alpha gene.

PubMed

Watanabe, Masashi; Tanaka, Kazuaki; Takizawa, Tatsuya; Segawa, Kazuhito; Neo, Sakurako; Tsuchiya, Ryo; Murata, Michiko; Murakami, Masaru; Hisasue, Masaharu

2014-01-01

A polymorphic tetranucleotide (GAAT)n microsatellite in the first intron of the canine tumor necrosis factor alpha (TNFA) gene was characterized in this study; 139 dogs were analyzed: 22 Beagles, 26 Chihuahuas, 20 Miniature Dachshunds, 24 Miniature Poodles, 22 Pembroke Welsh Corgis and 25 Shiba Inus. We detected the presence of the 4 alleles (GAAT)5, (GAAT)6, (GAAT)7 and (GAAT)8, including 9 of the 10 expected genotypes. The expected heterozygosity (He) and the polymorphic information content (PIC) value of this microsatellite locus varied from 0.389 to 0.749 and from 0.333 to 0.682, respectively, among the 6 breeds. The allelic frequency differed greatly among breeds, but this microsatellite marker was highly polymorphic and could be a useful marker for the canine TNFA gene.

Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

USGS Publications Warehouse

King, Timothy L.; Eackles, Michael S.; Reshetnikov, Andrey N.

2015-01-01

Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated

Evaluation of ploidy level and endoreduplication in carnation (Dianthus spp.).

PubMed

Agulló-Antón, María Ángeles; Olmos, Enrique; Pérez-Pérez, José Manuel; Acosta, Manuel

2013-03-01

Carnation (Dianthus caryophyllus L.) is one of the fifth most important ornamental species worldwide. Many desirable plant characteristics, such as big size, adaptation under stress, and intra or interspecific hybridization capability, are dependent on plant ploidy level. We optimized a quick flow cytometry method for DNA content determination in wild and cultivated carnation samples that allowed a systematic evaluation of ploidy levels in Dianthus species. The DNA content of different carnation cultivars and wild Dianthus species was determined using internal reference standards. The precise characterization of ploidy, endoreduplication and C-value of D. caryophyllus 'Master' makes it a suitable standard cultivar for ploidy level determination in other carnation cultivars. Mixoploidy was rigorously characterized in different regions of several organs from D. caryophyllus 'Master', which combined with a detailed morphological description suggested some distinctive developmental traits of this species. Both the number of endoreduplication cycles and the proportion of endopolyploid cells were highly variable in the petals among the cultivars studied, differently to the values found in leaves. Our results suggest a positive correlation between ploidy, cell size and petal size in cultivated carnation, which should be considered in breeding programs aimed to obtain new varieties with large flowers. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

The significance of tumor heterogeneity for prediction of DNA ploidy of prostate cancer.

PubMed

Häggarth, Lars; Auer, Gert; Busch, Christer; Norberg, Mona; Häggman, Michael; Egevad, Lars

2005-01-01

In a previous study, we mapped the ploidy heterogeneity of prostate cancer using flow cytometry in 676 tumor samples from 50 radical prostatectomy specimens. Ploidy heterogeneity was common (42% of tumors) and was found in all non-diploid tumors. The volume of non-diploid tumor was estimated and found to predict extra-prostatic extension and seminal vesicle invasion. The aim of this study was to evaluate the impact of tumor heterogeneity on preoperative ploidy assessment. In 50 men at least six core biopsies were taken before prostatectomy. Sections from biopsies with cancer were Feulgen-stained for image cytometry. After exclusion of biopsies with insufficient material, 123 histograms from 48 men (mean 2.6; range 1-7) remained for analysis. In 32 men, biopsies were diploid. In 16 men, at least one biopsy was non-diploid (14 tetraploid, two aneuploid) and 10 of them also had diploid biopsies. In 34 men (71%), the prostatectomy specimens were correctly predicted as being either diploid (48%) or non-diploid (23%). The sensitivity and specificity of biopsies for predicting non-diploid cancer were 55% and 82%, respectively, and the positive and negative predictive values were 69% and 72%, respectively. The ploidy status of tumors with and without ploidy heterogeneity was correctly predicted in 55% and 82% of cases, respectively (p=0.04). Biopsies underestimated ploidy in 9/20 tumors (45%) with heterogeneous ploidy status. Underestimation mainly occurred when one or two cores were analyzed. Preoperative prediction of the ploidy status of prostate cancer is hampered by tumor heterogeneity. Analysis of multiple biopsies is important for correct preoperative ploidy estimation.

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

PubMed

Lukoschek, V; Waycott, M; Keogh, J S

2008-07-01

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

Genetic diversity and population structure analysis of the tropical pasture grass Brachiaria humidicola based on microsatellites, cytogenetics, morphological traits, and geographical origin.

PubMed

Jungmann, L; Vigna, B B Z; Boldrini, K R; Sousa, A C B; do Valle, C B; Resende, R M S; Pagliarini, M S; Zucchi, M I; de Souza, A P

2010-09-01

Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out.

Microsatellite loci for the invasive colonial hydrozoan Cordylophora caspia

EPA Science Inventory

Cordylophora caspia, a colonial hydrozoan native to the Ponto-Caspian region, has become a common invader of both fresh and brackish water ecosystems of North America and Europe. Here we describe 11 polymorphic microsatellite loci for this species. Preliminary analyses indicate ...

Development of a High-Resolution Multi-Locus Microsatellite Typing Method for Colletotrichum gloeosporioides.

PubMed

Mehta, Nikita; Hagen, Ferry; Aamir, Sadaf; Singh, Sanjay K; Baghela, Abhishek

2017-12-01

Colletotrichum gloeosporioides is an economically important fungal pathogen causing substantial yield losses indifferent host plants. To understand the genetic diversity and molecular epidemiology of this fungus, we have developed a novel, high-resolution multi-locus microsatellite typing (MLMT) method. Bioinformatic analysis of C. gloeosporioides unannotated genome sequence yielded eight potential microsatellite loci, of which five, CG1 (GT) n , CG2 (GT1) n , CG3 (TC) n , CG4 (CT) n , and CG5 (CT1) n were selected for further study based on their universal amplification potential, reproducibility, and repeat number polymorphism. The selected microsatellites were used to analyze 31 strains of C. gloeosporioides isolated from 20 different host plants from India. All microsatellite loci were found to be polymorphic, and the approximate fragment sizes of microsatellite loci CG1, CG2, CG3, CG4, and CG5 were in ranges of 213-241, 197-227, 231-265, 209-275, and 132-188, respectively. Among the 31 isolates, 55 different genotypes were identified. The Simpson's index of diversity (D) values for the individual locus ranged from 0.79 to 0.92, with the D value of all combined five microsatellite loci being 0.99. Microsatellite data analysis revealed that isolates from Ocimum sanctum , Capsicum annuum (chili pepper), and Mangifera indica (mango) formed distinct clusters, therefore exhibited some level of correlation between certain genotypes and host. The developed MLMT method would be a powerful tool for studying the genetic diversity and any possible genotype-host correlation in C. gloeosporioides .

Ploidy Manipulation of Zebrafish Embryos with Heat Shock 2 Treatment

PubMed Central

Baars, Destiny L.; Pelegri, Francisco

2016-01-01

Manipulation of ploidy allows for useful transformations, such as diploids to tetraploids, or haploids to diploids. In the zebrafish Danio rerio, specifically the generation of homozygous gynogenetic diploids is useful in genetic analysis because it allows the direct production of homozygotes from a single heterozygous mother. This article describes a modified protocol for ploidy duplication based on a heat pulse during the first cell cycle, Heat Shock 2 (HS2). Through inhibition of centriole duplication, this method results in a precise cell division stall during the second cell cycle. The precise one-cycle division stall, coupled to unaffected DNA duplication, results in whole genome duplication. Protocols associated with this method include egg and sperm collection, UV treatment of sperm, in vitro fertilization and heat pulse to cause a one-cell cycle division delay and ploidy duplication. A modified version of this protocol could be applied to induce ploidy changes in other animal species. PMID:28060351

Microsatellite markers for Leucobryum boninense (Leucobryaceae), endemic to the Bonin Islands, Japan1

PubMed Central

Oguri, Emiko; Yamaguchi, Tomio; Kajita, Tadashi; Murakami, Noriaki

2013-01-01

• Premise of the study: Microsatellite primers were developed for Leucobryum boninense, endemic to the Bonin Islands, Japan, to investigate its level of genetic diversity and population genetic structure. • Methods and Results: Using next-generation sequencing, 21 primer sets were developed, among which nine loci were polymorphic in the populations of the Bonin Islands. Among these polymorphic loci, the number of alleles per locus ranged from two to 10 (mean = 3.444) and the expected heterozygosity ranged from 0.066 to 0.801 (mean = 0.338). • Conclusions: These results indicate the utility of the nine microsatellite markers that we developed for population genetic studies of L. boninense. PMID:25202543

Multiplexed microsatellite recovery using massively parallel sequencing

USGS Publications Warehouse

Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

Characterization of demographic expansions from pairwise comparisons of linked microsatellite haplotypes.

PubMed

Navascués, Miguel; Hardy, Olivier J; Burgarella, Concetta

2009-03-01

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.

Changes of ploidy during the Azotobacter vinelandii growth cycle.

PubMed Central

Maldonado, R; Jiménez, J; Casadesús, J

1994-01-01

The size of the Azotobacter vinelandii chromosome is approximately 4,700 kb, as calculated by pulsed-field electrophoretic separation of fragments digested with the rarely cutting endonucleases SpeI and SwaI. Surveys of DNA content per cell by flow cytometry indicated the existence of ploidy changes during the A. vinelandii growth cycle in rich medium. Early-exponential-phase cells have a ploidy level similar to that of Escherichia coli or Salmonella typhimurium (probably ca. four chromosomes per cell), but a continuous increase of DNA content per cell is observed during growth. Late-exponential-phase cells may contain > 40 chromosomes per cell, while cells in the early stationary stage may contain > 80 chromosomes per cell. In late-stationary-phase cultures, the DNA content per cell is even higher, probably over 100 chromosome equivalents per cell. A dramatic change is observed in old stationary-phase cultures, when the population of highly polyploid bacteria segregates cells with low ploidy. The DNA content of the latter cells resembles that of cysts, suggesting that the process may reflect the onset of cyst differentiation. Cells with low ploidy are also formed when old stationary-phase cultures are diluted into fresh medium. Addition of rifampin to exponential-phase cultures causes a rapid increase in DNA content, indicating that A. vinelandii initiates multiple rounds of chromosome replication per cell division. Growth in minimal medium does not result in the spectacular changes of ploidy observed during rapid growth; this observation suggests that the polyploidy of A. vinelandii may not exist outside the laboratory. Images PMID:8021173

Use of eyeballs for establishing ploidy of Asian carp

USGS Publications Warehouse

Jenkins, J.A.; Thomas, R.G.

2007-01-01

Grass carp Ctenopharyngodon idella, silver carp Hypophthalmichthys molitrix, and bighead carp H. nobilis are now established and relatively common in the Mississippi and Atchafalaya rivers. Commercial fishers of Louisiana's large rivers report recurrent catches of grass carp, and the frequency of bighead carp and silver carp catch is increasing. Twelve black carp Mylopharyngodon piceus were recently captured from the Mississippi and Atchafalaya River system, and 10 were analyzed for ploidy. By using the methods described herein, all 10 fish were determined to be diploid. Such correct identifications of ploidy of feral Asian carp species, as well as other species, would provide science-based information constructive for meeting reporting requirements, tracking fish movements, and forecasting expansion of species distribution. To investigate the postmortem period for sample collection and to lessen demands on field operations for obtaining samples, a laboratory study was performed to determine the length of time for which eyeballs from postmortem black carp could be used for ploidy determinations. Acquiring eyes rather than blood is simpler and quicker and requires no special supplies. An internal DNA reference standard with a documented genome size, including erythrocytes from diploid black carp or Nile tilapia Oreochromis niloticus, was analyzed simultaneously with cells from seven known triploid black carp to assess ploidy through 12 d after extraction. Ploidy determinations were reliable through 8 d postmortem. The field process entails excision of an eyeball, storage in a physiological buffer, and shipment within 8 d at refrigeration temperatures (4??C) to the laboratory for analysis by flow cytometry. ?? Copyright by the American Fisheries Society 2007.

Population Structure of Candida parapsilosis: No Genetic Difference Between French and Uruguayan Isolates Using Microsatellite Length Polymorphism.

PubMed

Desnos-Ollivier, Marie; Bórmida, Victoria; Poirier, Philippe; Nourrisson, Céline; Pan, Dinorah; Bretagne, Stéphane; Puime, Andrès; Dromer, Françoise

2018-04-01

Candida parapsilosis is a human commensal yeast, frequently involved in infection worldwide and especially in neonates. It is the second species responsible for bloodstream infections in Uruguay and the third species in France. We were interested in knowing whether the population structure of isolates responsible for candidemia in France and in Uruguay was different. Genotyping methods based on microsatellite length polymorphism (MLP) have been described and are especially used for investigation of local outbreaks. We therefore determined the genotypes of 159 C. parapsilosis isolates recovered from 122 patients (84 French patients from 43 hospitals and 38 Uruguayan patients from 10 hospitals) using three microsatellites markers previously described. Our results confirmed that C. parapsilosis population has a high genetic diversity, clonal inheritance and that majority of patients were infected by a single isolate. But we described recurrent infections due to related or unrelated genotypes resulting from isolates harboring loss or gain of heterozygosity. We also described three cases of coinfections due to unrelated genotypes. We did not uncover geographic specificity but observed two linked genotypes that seem to be associated with voriconazole resistance. Finally, among eight isolates involved in grouped cases, the genotypes were similar in six cases supporting the hypothesis of inter-patient transmission. These results confirmed the usefulness of performing MLP genotyping analysis for grouped cases of C. parapsilosis isolates in order to reinforce preventive hygiene measures.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.

PubMed

Gertz, E Michael; Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

PubMed Central

Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A.

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees. PMID

Molecular characterization of allelic variants of (GATA)n microsatellite loci in parthenogenetic lizards Darevskia unisexualis (Lacertidae).

PubMed

Korchagin, V I; Badaeva, T N; Tokarskaya, O N; Martirosyan, I A; Darevsky, I S; Ryskov, A P

2007-05-01

Populations of parthenogenetic lizards of the genus Darevskia consist of genetically identical animals, and represent a unique model for studying the molecular mechanisms underlying the variability and evolution of hypervariable DNA repeats. As unisexual lineages, parthenogenetic lizards are characterized by some level of genetic diversity at microsatellite loci. We cloned and sequenced a number of (GATA)n microsatellite loci of Darevskia unisexualis. PCR products from these loci were also sequenced and the degree of intraspecific polymorphism was assessed. Among the five (GATA)n loci analysed, two (Du215 and Du281) were polymorphic. Cross-species analysis of Du215 and Du281 indicate that the priming sites at the D. unisexualis loci are conserved in the bisexual parental species, D. raddei and D. valentini. Sequencing the PCR products amplified from Du215 and Du281 and from monomorphic Du323 showed that allelic differences at the polymorphic loci are caused by microsatellite mutations and by point mutations in the flanking regions. The haplotypes identified among the allelic variants of Du281 and among its orthologues in the parental species provide new evidence of the cross-species origin of D. unisexualis. To our knowledge, these data are the first to characterize the nucleotide sequences of allelic variants at microsatellite loci within parthenogenetic vertebrate animals.

Microsatellites evolve more rapidly in humans than in chimpanzees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubinsztein, D.C.; Leggo, J.; Amos, W.

1995-12-10

Microsatellites are highly polymorphic markers consisting of varying numbers of tandem repeats. At different loci, these repeats can consist of one to five nucleotides. Microsatellites have been used in many fields of genetics, including genetic mapping, linkage disequilibrium analyses, forensic studies, and population genetics. It is important that we understand their mutational processes better so that they can be exploited optimally for studies of human diversity and evolutionary genetics. We have analyzed 24 microsatellite loci in chimpanzees, East Anglians, and Sub-Saharan Africans. The stepwise-weighted genetic distances between the humans and the chimpanzees and between the two human populations were calculatedmore » according to the method described by Deka et al. The ratio of the genetic distances between the chimpanzees and the humans relative to that between the Africans and the East Anglians was more than 10 times smaller than expected. This suggests that microsatellites have evolved more rapidly in humans than in chimpanzees. 12 refs., 1 tab.« less

Development of microsatellite primers of the largest seagrass, Enhalus acoroides (Hydrocharitaceae).

PubMed

Gao, Hui; Jiang, Kai; Geng, Yan; Chen, Xiao-Yong

2012-03-01

Microsatellite primers were developed for the seagrass Enhalus acoroides to investigate genetic variation and identify clonal structure. Four polymorphic loci and 32 monomorphic loci were developed in E. acoroides. Two to four alleles per locus were observed at the polymorphic loci across 60 individuals of two E. acoroides populations. The observed and expected heterozygosities within populations ranged from 0.100 to 0.5667 and from 0.0977 to 0.5079, respectively. Our study revealed very low polymorphism in E. acoroides, even at the polymorphic loci. Nevertheless, these primers are a useful tool to study genetic variation, clonal structure, and mating system.

Application of microsatellite primers developed for Polistes in the independent-founding wasp Polists satan Bequaert (Hymenoptera: Vespidae).

PubMed

Komatsu, K; Mateus, S; Zucchi, R; Nascimento, F; Kudô, K

2012-06-01

Microsatellite primers developed for a given species are sometimes useful for another in the same genus and in other genera within the same family, making possible to search for pre-existing suitable primers in the databanks such as GenBank. We examined whether existing primers developed for Polistes could be used for Polistes satan Bequaert. We tested 50 microsatellite primers from three Polistes species and found that six microsatellite loci show polymorphism in size in P. satan. These six loci were highly polymorphic, having four to 15 alleles in P. satan with an expected heterozygosity of 0.525-0.832. These loci can be used to study parameters concerning genetic relatedness such as social interactions in colonies and genetic conflicts of interest among nestmate individuals.

Development, characterization, and cross-amplification of 16 microsatellite primers for Atriplex tatarica (Amaranthaceae)1

PubMed Central

Kondrysová, Eva; Krak, Karol; Mandák, Bohumil

2017-01-01

Premise of the study: Microsatellite primers were developed to characterize the genetic diversity and structure of the annual herb Atriplex tatarica (Amaranthaceae) and to facilitate ecological and evolutionary studies of A. tatarica and its relatives. Methods and Results: Sixteen novel microsatellite primers were developed for A. tatarica based on high-throughput sequencing of enriched libraries. All markers were polymorphic, with the number of alleles per locus ranging from three to 25 and observed and expected heterozygosity ranging from 0.08 to 0.74 and 0.10 to 0.87, respectively. In addition, some of these loci were successfully amplified and showed polymorphisms in four Atriplex and seven Chenopodium species. Conclusions: The microsatellite markers published here will be useful in assessing genetic diversity, structure, and gene flow within and across populations of A. tatarica, as well as in other species of Atriplex and the related genus Chenopodium. PMID:29188148

Development and characterization of 32 microsatellite loci in Genipa americana (Rubiaceae)1

PubMed Central

Manoel, Ricardo O.; Freitas, Miguel L. M.; Barreto, Mariana A.; Moraes, Mário L. T.; Souza, Anete P.; Sebbenn, Alexandre M.

2014-01-01

• Premise of the study: Microsatellite primers were developed for the tree species Genipa americana (Rubiaceae) for further population genetic studies. • Methods and Results: We identified 144 clones containing 65 repeat motifs from a genomic library enriched for (CT)8 and (GT)8 motifs. Primer pairs were developed for 32 microsatellite loci and validated in 40 individuals of two natural G. americana populations. Seventeen loci were polymorphic, revealing from three to seven alleles per locus. The observed and expected heterozygosities ranged from 0.24 to 1.00 and from 0.22 to 0.78, respectively. • Conclusions: The 17 primers identified as polymorphic loci are suitable to study the genetic diversity and structure, mating system, and gene flow in G. americana. PMID:25202610

A microsatellite genetic linkage map of black rockfish ( Sebastes schlegeli)

NASA Astrophysics Data System (ADS)

Chu, Guannan; Jiang, Liming; He, Yan; Yu, Haiyang; Wang, Zhigang; Jiang, Haibin; Zhang, Quanqi

2014-12-01

Ovoviviparous black rockfish ( Sebastes schlegeli) is an important marine fish species for aquaculture and fisheries in China. Genetic information of this species is scarce because of the lack of microsatellite markers. In this study, a large number of microsatellite markers of black rockfish were isolated by constructing microsatellite-enriched libraries. Female- and male-specific genetic linkage maps were constructed using 435 microsatellite markers genotyped in a full-sib family of the fish species. The female linkage map contained 140 microsatellite markers, in which 23 linkage groups had a total genetic length of 1334.1 cM and average inter-marker space of 13.3 cM. The male linkage map contained 156 microsatellite markers, in which 25 linkage groups had a total genetic length of 1359.6 cM and average inter-marker distance of 12.4 cM. The genome coverage of the female and male linkage maps was 68.6% and 69.3%, respectively. The female-to-male ratio of the recombination rate was approximately 1.07:1 in adjacent microsatellite markers. This paper presents the first genetic linkage map of microsatellites in black rockfish. The collection of polymorphic markers and sex-specific linkage maps of black rockfish could be useful for further investigations on parental assignment, population genetics, quantitative trait loci mapping, and marker-assisted selection in related breeding programs.

Characterization of microsatellite markers in eastern white pine

Treesearch

C. S. Echt; P. May-Marquardt; M. Hseih; R. Zahorchak

1996-01-01

An enrichment cloning method was evaluated for the isolation of microsatellite loci from eastern white pine and the resulting markers were examined for polymorphisms. A 200-fold enrichment was achieved for highly abundant (AC)n repeats, but for much less abundant (ACAG)n repeats an enrichment of only 20-fold was obtained....

Characterization of microsatellites from a genome of Venturia carpophila

USDA-ARS?s Scientific Manuscript database

Microsatellites were mined from a genome of Venturia carpophila and 192 were selected to screen 39 isolates of the fungus collected from peach and nectarine in the southeastern USA. Reliable, polymorphic amplicons were produced by 32 of the selected primers. A preliminary analysis of the genetic div...

Isolation and characterization of microsatellite loci in Greater Sage-Grouse (Centlocerus urophasianus)

USGS Publications Warehouse

Taylor, S.E.; Oyler-McCance, S.J.; Quinn, T.W.

2003-01-01

Primers for five polymorphic microsatellite loci were developed for Greater Sage-Grouse (Centrocercus urophasianus) using an enrichment/detection protocol. The high level of polymorphism (nine to 33 alleles) suggests that these loci will be applicable for investigating mating systems and paternity analysis as well as population genetics. Cross-species amplification was successful for each locus in at least two other galliform species.

Multilocus microsatellite typing shows three different genetic clusters of Leishmania major in Iran.

PubMed

Mahnaz, Tashakori; Al-Jawabreh, Amer; Kuhls, Katrin; Schönian, Gabriele

2011-10-01

Ten polymorphic microsatellite markers were used to analyse 25 strains of Leishmania major collected from cutaneous leishmaniasis cases in different endemic areas in Iran. Nine of the markers were polymorphic, revealing 21 different genotypes. The data displayed significant microsatellite polymorphism with rare allelic heterozygosity. Bayesian statistic and distance based analyses identified three genetic clusters among the 25 strains analysed. Cluster I represented mainly strains isolated in the west and south-west of Iran, with the exception of four strains originating from central Iran. Cluster II comprised strains from the central part of Iran, and cluster III included only strains from north Iran. The geographical distribution of L. major in Iran was supported by comparing the microsatellite profiles of the 25 Iranian strains to those of 105 strains collected in 19 Asian and African countries. The Iranian clusters I and II were separated from three previously described populations comprising strains from Africa, the Middle East and Central Asia whereas cluster III grouped together with the Central Asian population. The considerable genetic variability of L. major might be related to the existence of different populations of Phlebotomus papatasi and/or to differences in reservoir host abundance in different parts of Iran. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys.

PubMed

Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

2015-01-26

Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species.

Ploidally antagonistic selection maintains stable genetic polymorphism.

PubMed

Immler, Simone; Arnqvist, Göran; Otto, Sarah Perin

2012-01-01

Understanding the maintenance of genetic variation in the face of selection remains a key issue in evolutionary biology. One potential mechanism for the maintenance of genetic variation is opposing selection during the diploid and haploid stages of biphasic life cycles universal among eukaryotic sexual organisms. If haploid and diploid gene expression both occur, selection can act in each phase, potentially in opposing directions. In addition, sex-specific selection during haploid phases is likely simply because male and female gametophytes/gametes tend to have contrasting life histories. We explored the potential for the maintenance of a stable polymorphism under ploidally antagonistic as well as sex-specific selection. Furthermore, we examined the role of the chromosomal location of alleles (autosomal or sex-linked). Our analyses show that the most permissible conditions for the maintenance of polymorphism occur under negative ploidy-by-sex interactions, where stronger selection for an allele in female than male diploids is coupled with weaker selection against the allele in female than male haploids. Such ploidy-by-sex interactions also promote allele frequency differences between the sexes. With constant fitness, ploidally antagonistic selection can maintain stable polymorphisms for autosomal and X-linked genes but not for Y-linked genes. We discuss the implications of our results and outline a number of biological settings where the scenarios modeled may apply. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing.

PubMed

Jorge, Paulo H; Mastrochirico-Filho, Vito A; Hata, Milene E; Mendes, Natália J; Ariede, Raquel B; de Freitas, Milena Vieira; Vera, Manuel; Porto-Foresti, Fábio; Hashimoto, Diogo T

2018-01-01

The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme.

Characterization of microsatellite DNA markers for the alligator snapping turtle, Macrochelys temminckii: Primer note

USGS Publications Warehouse

Hackler, J.C.; Van Den Bussche, Ronald A.; Leslie, David M.

2007-01-01

Two trinucleotide and seven tetranucleotide microsatellite loci were isolated from an alligator snapping turtle Macrochelys temminckii. To assess the degree of variability in these nine microsatellite loci, we genotyped 174 individuals collected from eight river drainage basins in the southeastern USA. These markers revealed a moderate degree of allelic diversity (six to 16 alleles per locus) and observed heterozygosity (0.166-0.686). These polymorphic microsatellite loci provide powerful tools for population genetic studies for a species that is afforded some level of conservation protection in every state in which it occurs. ?? 2006 The Authors.

Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species.

PubMed

Lee, Gi-An; Song, Jae Young; Choi, Heh-Ran; Chung, Jong-Wook; Jeon, Young-Ah; Lee, Jung-Ro; Ma, Kyung-Ho; Lee, Myung-Chul

2015-04-10

The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.).

PubMed

Harmon, Monica; Lane, Thomas; Staton, Margaret; Coggeshall, Mark V; Best, Teodora; Chen, Chien-Chih; Liang, Haiying; Zembower, Nicole; Drautz-Moses, Daniela I; Hwee, Yap Zhei; Schuster, Stephan C; Schlarbaum, Scott E; Carlson, John E; Gailing, Oliver

2017-08-08

Sugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple. A set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species. Genic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change.

Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis

PubMed Central

Cao, Li-Jun; Li, Ze-Min; Wang, Ze-Hua; Zhu, Liang; Gong, Ya-Jun; Chen, Min; Wei, Shu-Jun

2016-01-01

Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy–Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies. PMID:27197749

Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis.

PubMed

Cao, Li-Jun; Li, Ze-Min; Wang, Ze-Hua; Zhu, Liang; Gong, Ya-Jun; Chen, Min; Wei, Shu-Jun

2016-05-20

Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy-Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies.

Utility of a Fluorescence Microscopy Imaging System for Analyzing the DNA Ploidy of Pathological Megakaryocytes Including 5q- Syndrome.

PubMed

Nakahara, Takako; Suemori, Shinichiro; Tsujioka, Takayuki; Kataoka, Mikio; Kataoka, Hiromi; Shibakura, Misako; Tohyama, Kaoru

2018-06-01

To investigate megakaryocyte (MK) DNA ploidy in various hematological diseases, fluorescence microscopy imaging system (FMI) can be used to analyze DNA ploidy with cell morphology at the single-cell level by using specialized image-processing software. Here we compared DNA ploidy obtained by FMI measured with that obtained flow cytometry (FCM). With FMI, we could evaluate the DNA ploidy in long-term preserved bone marrow smear samples after staining. We next analyzed the MK DNA ploidy in 42 bone marrow smear samples including 26 myeloid neoplasm cases, and we compared the DNA ploidy and platelet counts in the patients' peripheral blood; the production of platelets was significantly high compared to DNA ploidy in the myeloproliferative neoplasms group. The FMI method revealed that the patients with 5q- syndrome exhibited relatively low DNA ploidy despite high platelet counts, and this result suggested that increased DNA ploidy is not indispensable to abundant platelet production. The FMI method for DNA ploidy will be a useful tool to clarify the relationship between DNA ploidy and platelet production by MKs.

Date Palm Genetic Diversity Analysis Using Microsatellite Polymorphism.

PubMed

Khierallah, Hussam S M; Bader, Saleh M; Hamwieh, Alladin; Baum, Michael

2017-01-01

Date palm (Phoenix dactylifera L.) is considered one of the great socioeconomic resources in the Middle East and the Arab regions. The tree has been and still is at the center of the comprehensive agricultural development. The number of known date palm cultivars, distributed worldwide, is approximately 3000. The success of genetic diversity conservation or any breeding program depends on an understanding of the amount and distribution of the genetic variation already in existence in the genetic pool. Development of suitable DNA molecular markers for this tree may allow researchers to estimate genetic diversity, which will ultimately lead to the genetic conservation of date palm. Simple sequence repeats (SSRs) are DNA strands, consisting of tandemly repeated mono-, di-, tri-, tetra-, or penta-nucleotide units that are arranged throughout the genomes of most eukaryotic species. Microsatellite markers, developed from genomic libraries, belong to either the transcribed region or the non-transcribed region of the genome, and there is rarely available information on their functions. Microsatellite sequences are especially suited to distinguish closely related genotypes due to a high degree of variability making them ideally suitable in population studies and the identification of closely related cultivars. This chapter focuses on the methods employed to characterize date palm genotypes using SSR markers.

Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species.

PubMed

Behura, Susanta K; Severson, David W

2015-02-01

We present a detailed genome-wide comparative study of motif mismatches of microsatellites among 20 insect species representing five taxonomic orders. The results show that varying proportions (∼15-46%) of microsatellites identified in these species are imperfect in motif structure, and that they also vary in chromosomal distribution within genomes. It was observed that the genomic abundance of imperfect repeats is significantly associated with the length and number of motif mismatches of microsatellites. Furthermore, microsatellites with a higher number of mismatches tend to have lower abundance in the genome, suggesting that sequence heterogeneity of repeat motifs is a key determinant of genomic abundance of microsatellites. This relationship seems to be a general feature of microsatellites even in unrelated species such as yeast, roundworm, mouse and human. We provide a mechanistic explanation of the evolutionary link between motif heterogeneity and genomic abundance of microsatellites by examining the patterns of motif mismatches and allele sequences of single-nucleotide polymorphisms identified within microsatellite loci. Using Drosophila Reference Genetic Panel data, we further show that pattern of allelic variation modulates motif heterogeneity of microsatellites, and provide estimates of allele age of specific imperfect microsatellites found within protein-coding genes. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Isolation and characterization of microsatellite markers for Jasminum sambac (Oleaceae) using Illumina shotgun sequencing.

PubMed

Li, Yong; Zhang, Weirui

2015-10-01

Microsatellite markers of Jasminum sambac (Oleaceae) were isolated to investigate wild germplasm resources and provide markers for breeding. Illumina sequencing was used to isolate microsatellite markers from the transcriptome of J. sambac. A total of 1322 microsatellites were identified from 49,772 assembled unigenes. One hundred primer pairs were randomly selected to verify primer amplification efficiency. Out of these tested primer pairs, 31 were successfully amplified: 18 primer pairs yielded a single allele, seven exhibited fixed heterozygosity with two alleles, and only six displayed polymorphisms. This study obtained the first set of microsatellite markers for J. sambac, which will be helpful for the assessment of wild germplasm resources and the development of molecular marker-assisted breeding.

Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database

PubMed Central

Scaglione, Davide; Acquadro, Alberto; Portis, Ezio; Taylor, Christopher A; Lanteri, Sergio; Knapp, Steven J

2009-01-01

Background The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. Results A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. Conclusion EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species. PMID:19785740

CHARACTERIZATION OF MICROSATELLITE LOCI IN THE EUROPEAN GREEN CRAB (CARCINUS MAENAS)

EPA Science Inventory

Carcinus maenas (Decapoda: Portunidae) has proven a highly successful invasive marine species whose potential economic and ecological impacts are of great concern worldwide. Here, we characterize fourteen polymorphic microsatellite loci in C. maenas and its sister species C. Ae...

Novel microsatellite development and characterization for Phacelia formosula (Hydrophyllaceae).

PubMed

Riser, James P; Schwabe, Anna L; Neale, Jennifer Ramp

2017-07-01

Microsatellite primers were developed to characterize genetic diversity and structuring in the genus Phacelia (Hydrophyllaceae) and to further conservation efforts for P. formosula . Fifteen novel microsatellite primers were developed for P. formosula . These were characterized for genetic variation in three separate P. formosula populations. Two to nine alleles were found per locus. Overall observed heterozygosity and expected heterozygosity ranged from 0.000 to 0.800 and 0.000 to 0.840, respectively. Additionally, these loci were successfully amplified and showed polymorphism in P. gina-glenneae and a potential new Phacelia species. These microsatellite markers will be useful in assessing genetic diversity, structuring, and gene flow within and among populations of the rare P. formosula , in addition to related Phacelia species. These markers will provide important genetic data needed for appropriate conservation and management of these rare plants.

Characterization of microsatellite markers in eastern white pine

Treesearch

Craig S. Echt; P. May-Marquardt; M. Hseih; R. Zahorchak

1996-01-01

An enrichment cloning method was evaluated for the isolation of microsatellite loci from eastern white pine and the resulting markers were examined for polymorphisms. A 200-fold enrichment was achieved for highly abundant (AC), repeats, but for much less abundant (ACAG), repeats an enrichment of only 20-fold was obtained. Using a single set of PCR conditions, 19...

Development and characterization of 27 microsatellite markers for the mangrove fern, Acrostichum aureum (Pteridaceae).

PubMed

Yamamoto, Takashi; Tsuda, Yoshiaki; Mori, Gustavo Maruyama; Cruz, Mariana Vargas; Shinmura, Yoshimi; Wee, Alison K S; Takayama, Koji; Asakawa, Takeshi; Yamakawa, Takeru; Suleiman, Monica; Núñez-Farfán, Juan; Webb, Edward L; Watano, Yasuyuki; Kajita, Tadashi

2016-09-01

Twenty-seven nuclear microsatellite markers were developed for the mangrove fern, Acrostichum aureum (Pteridaceae), to investigate the genetic structure and demographic history of the only pantropical mangrove plant. Fifty-six A. aureum individuals from three populations were sampled and genotyped to characterize the 27 loci. The number of alleles and expected heterozygosity ranged from one to 15 and 0.000 to 0.893, respectively. Across the 26 polymorphic loci, the Malaysian population showed much higher levels of polymorphism compared to the other two populations in Guam and Brazil. Cross-amplification tests in the other two species from the genus determined that seven and six loci were amplifiable in A. danaeifolium and A. speciosum, respectively. The 26 polymorphic microsatellite markers will be useful for future studies investigating the genetic structure and demographic history of of A. aureum, which has the widest distributional range of all mangrove plants.

Distant hybridization leads to different ploidy fishes.

PubMed

Liu, ShaoJun

2010-04-01

Distant hybridization makes it possible to transfer the genome of one species to another, which results in changes in phenotypes and genotypes of the progenies. This study shows that distant hybridization or the combination of this method with gynogenesis or androgenesis lead to different ploidy fishes with genetic variation, including fertile tetraploid hybrids, sterile triploid hybrids, fertile diploid hybrids, fertile diploid gynogenetic fish, and their derived progenies. The formations of the different ploidy fishes depend on the genetic relationship between the parents. In this study, several types of distant hybridization, including red crucian carp (Carassius auratus red var.) (2n=100, abbreviated as RCC) (female) x common carp (Cyprinus carpio L.) (2n=100, abbreviated as CC) (male), and RCC (2n=100) (female) x blunt snout bream (Megalobrama amblycephala) (2n=48, abbreviated as BSB) (male) are described. In the distant hybridization of RCC (female) x CC (male), bisexual fertile F(3)-F(18) allotetraploid hybrids (4n=200, abbreviated as 4nAT) were formed. The diploid hybrid eggs and diploid sperm generated by the females and males of 4nAT developed into diploid gynogenetic hybrids and diploid androgenetic hybrids, respectively, by gynogenesis and androgenesis, without treatment for doubling the chromosome. Improved tetraploid hybrids and improved diploid fishes with genetic variation were derived from the gynogenetic hybrid line. The improved diploid fishes included the high-body RCC and high-body goldfish. The formation of the tetraploid hybrids was related to the occurrence of unreduced gametes generated from the diploid hybrids, which involved in premeiotic endoreduplication, endomitosis, or fusion of germ cells. The sterile triploid hybrids (3n=150) were produced on a large scale by crossing the males of tetraploid hybrids with females of diploid fish (2n=100). In another distant hybridization of RCC (female) x BSB (male), different ploidy fishes were

Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing

PubMed Central

Wang, Jinjin; Yu, Xiaomu; Zhao, Kai; Zhang, Yaoguang; Tong, Jingou; Peng, Zuogang

2012-01-01

Megalobrama pellegrini is an endemic fish species found in the upper Yangtze River basin in China. This species has become endangered due to the construction of the Three Gorges Dam and overfishing. However, the available genetic data for this species is limited. Here, we developed 26 polymorphic microsatellite markers from the M. pellegrini genome using next-generation sequencing techniques. A total of 257,497 raw reads were obtained from a quarter-plate run on 454 GS-FLX titanium platforms and 49,811 unique sequences were generated with an average length of 404 bp; 24,522 (49.2%) sequences contained microsatellite repeats. Of the 53 loci screened, 33 were amplified successfully and 26 were polymorphic. The genetic diversity in M. pellegrini was moderate, with an average of 3.08 alleles per locus, and the mean observed and expected heterozygosity were 0.47 and 0.51, respectively. In addition, we tested cross-species amplification for all 33 loci in four additional breams: M. amblycephala, M. skolkovii, M. terminalis, and Sinibrama wui. The cross-species amplification showed a significant high level of transferability (79%–97%), which might be due to their dramatically close genetic relationships. The polymorphic microsatellites developed in the current study will not only contribute to further conservation genetic studies and parentage analyses of this endangered species, but also facilitate future work on the other closely related species. PMID:22489139

CHARACTERIZATION OF MICROSATELLITE LOCI IN THE WIDELY INTRODUCED ESTUARINE ANEMONE NEMATOSTELLA VECTENSIS

EPA Science Inventory

We characterized ten polymorphic microsatellite loci from Nematostella vectensis, a burrowing anemone recently introduced to estuaries along the Pacific coast of North America and the southeast coast of England. Preliminary results indicate high variability and significant depar...

Change in ploidy status from hyperdiploid to near-tetraploid in multiple myeloma associated with bortezomib/lenalidomide resistance.

PubMed

Pavlistova, Lenka; Zemanova, Zuzana; Sarova, Iveta; Lhotska, Halka; Berkova, Adela; Spicka, Ivan; Michalova, Kyra

2014-01-01

Ploidy is an important prognostic factor in the risk stratification of multiple myeloma (MM) patients. Patients with MM can be divided into two groups according to the modal number of chromosomes: nonhyperdiploid (NH-MM) and hyperdiploid (H-MM), which has a more favorable outcome. The two ploidy groups represent two different oncogenetic pathways determined at the premalignant stage. The ploidy subtype also persists during the course of the disease, even during progression after the therapy, with only very rare cases of ploidy conversion. The clinical significance of ploidy conversion and its relation to drug resistance have been previously discussed. Here, we describe a female MM patient with a rare change in her ploidy status from H-MM to NH-MM, detected by cytogenetic and molecular cytogenetic examinations of consecutive bone marrow aspirates. We hypothesize that ploidy conversion (from H-MM to NH-MM) is associated with disease progression and acquired resistance to bortezomib/lenalidomide therapy. Copyright © 2014 Elsevier Inc. All rights reserved.

[Genetic diversity of microsatellite loci in captive Amur tigers].

PubMed

Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

2004-09-01

The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten

New microsatellites revealed strong gene flow among populations of a new outbreak pest, Athetis lepigone (Möschler).

PubMed

Zhu, W-C; Sun, J-T; Dai, J; Huang, J-R; Chen, L; Hong, X-Y

2017-11-27

Athetis lepigone (Möschler) (Lepidoptera: Noctuidae) is a new outbreak pest in China. Consequently, it is unclear whether the emergence and spread of the outbreak of this pest are triggered by rapid in situ population size increases in each outbreak area, or by immigrants from a potential source area in China. In order to explore the outbreak process of this pest through a population genetics approach, we developed ten novel polymorphic expressed sequence tags (EST)-derived microsatellites. These new microsatellites had moderately high levels of polymorphism in the tested population. The number of alleles per locus ranged from 3 to 19, with an average of 8.6, and the expected heterozygosity ranged from 0.269 to 0.783. A preliminary population genetic analysis using these new microsatellites revealed a lack of population genetic structure in natural populations of A. lepigone. The estimates of recent migration rate revealed strong gene flow among populations. In conclusion, our study developed the first set of EST-microsatellite markers and shed a new light on the population genetic structure of this pest in China.

Genomic Microsatellites as Evolutionary Chronometers: A Test in Wild Cats

PubMed Central

Driscoll, Carlos A.; Menotti-Raymond, Marilyn; Nelson, George; Goldstein, David; O'Brien, Stephen J.

2002-01-01

Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of historic population bottlenecks and founder effects. The observed rate of reconstruction of new alleles plus the growth in the breadth of microsatellite allele size (variance) was used here to develop genomic estimates of time intervals following historic founder events in cheetahs (12,000 yr ago), in North American pumas (10,000–17,000 yr ago), and in Asiatic lions of the Gir Forest (1000–4000 yr ago). [Supplemental material available online at http://rex.nci.nih.gov/lgd/front_page.htm and at http://www.genome.org.] PMID:11875029

Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs.

PubMed

Dufresnes, Christophe; Brelsford, Alan; Béziers, Paul; Perrin, Nicolas

2014-07-01

A simple way to quickly optimize microsatellites in nonmodel organisms is to reuse loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA vs. 17 loci derived from a transcriptome, across nine species of tree frogs (Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My, respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites seems an optimal approach for multispecies surveys (e.g. analyses of hybrid zones, comparative linkage mapping), whereas anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palaearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation. © 2013 John Wiley & Sons Ltd.

Correlation of DNA Ploidy with Progression of Cervical Cancer

PubMed Central

Singh, M.; Mehrotra, S.; Kalra, N.; Singh, U.; Shukla, Y.

2008-01-01

The majority of squamous cell carcinomas of cervix are preceded by visible changes in the cervix, most often detected by cervical smear. As cervical cancer is preceded by long precancerous stages, identification of the high-risk population through detection of DNA ploidy may be of importance in effective management of this disease. Here we attempted to correlate aneuploid DNA patterns and their influence on biological behavior of flow-cytometry analysis of DNA ploidy which was carried out in cytologically diagnosed cases of mild (79), moderate (36), and severe (12) dysplasia, as well as “atypical squamous cells of unknown significance (ASCUS)” (57) along with controls (69), in order to understand its importance in malignant progression of disease. Cytologically diagnosed dysplasias, which were employed for DNA ploidy studies, 39 mild, 28 moderate, and 11 severe dysplasia cases were found to be aneuploid. Out of the 69 control subjects, 6 cases showed aneuploidy pattern and the rest 63 subjects were diploid. An aneuploidy pattern was observed in 8 out of 57 cases of cytologically evaluated ASCUS. The results of the followup studies showed that aberrant DNA content reliably predicts the occurrence of squamous cell carcinoma in cervical smear. Flow cytometric analysis of DNA ploidy may provide a strategic diagnostic tool for early detection of carcinoma cervix. Therefore, it is a concept of an HPV screening with reflex cytology in combination with DNA flow cytometry to detect progressive lesions with the greatest possible sensitivity and specificity. PMID:20445775

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Zhang, Shuo; Tang, Chanjuan; Zhao, Qiang; Li, Jing; Yang, Lifang; Qie, Lufeng; Fan, Xingke; Li, Lin; Zhang, Ning; Zhao, Meicheng; Liu, Xiaotong; Chai, Yang; Zhang, Xue; Wang, Hailong; Li, Yingtao; Li, Wen; Zhi, Hui; Jia, Guanqing; Diao, Xianmin

2014-01-28

Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species. A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1' by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei's genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective. A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.

Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats.

PubMed

Poissant, J; Shafer, A B A; Davis, C S; Mainguy, J; Hogg, J T; Côté, S D; Coltman, D W

2009-07-01

We tested for cross-species amplification of microsatellite loci located throughout the domestic sheep (Ovis aries) genome in two north American mountain ungulates (bighorn sheep, Ovis canadensis, and mountain goats, Oreamnos americanus). We identified 247 new polymorphic markers in bighorn sheep (≥ 3 alleles in one of two study populations) and 149 in mountain goats (≥ 2 alleles in a single study population) using 648 and 576 primer pairs, respectively. Our efforts increased the number of available polymorphic microsatellite markers to 327 for bighorn sheep and 180 for mountain goats. The average distance between successive polymorphic bighorn sheep and mountain goat markers inferred from the Australian domestic sheep genome linkage map (mean ± 1 SD) was 11.9 ± 9.2 and 15.8 ± 13.8 centimorgans, respectively. The development of genomic resources in these wildlife species enables future studies of the genetic architecture of trait variation. © 2009 Blackwell Publishing Ltd.

Development and characterization of microsatellite loci for the endangered scrub Lupine, Lupinus aridorum (Fabaceae)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ricono, Angela; Bupp, Glen; Peterson, Cheryl

Microsatellite primers were developed in scrub lupine ( Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [ L. diffusus] and Gulf Coast lupine [ L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. In conclusion, these loci are the first developed for Florida species of lupine and willmore » be used to determine differentiation among species and to aid in conservation of the endangered scrub lupine.« less

Development and characterization of microsatellite loci for the endangered scrub Lupine, Lupinus aridorum (Fabaceae)

DOE PAGES

Ricono, Angela; Bupp, Glen; Peterson, Cheryl; ...

2015-04-01

Microsatellite primers were developed in scrub lupine ( Lupinus aridorum, Fabaceae), an endemic species to Florida that is listed as endangered in the United States, to assess connectivity among populations, identify hybrids, and examine genetic diversity. We isolated and characterized 12 microsatellite loci polymorphic in scrub lupine or in closely related species (i.e., sky-blue lupine [ L. diffusus] and Gulf Coast lupine [ L. westianus]). Loci showed low to moderate polymorphism, ranging from two to 14 alleles per locus and 0.01 to 0.86 observed heterozygosity. In conclusion, these loci are the first developed for Florida species of lupine and willmore » be used to determine differentiation among species and to aid in conservation of the endangered scrub lupine.« less

Characterization of microsatellite loci for an Australian epiphytic orchid, Dendrobium calamiforme, using illumina sequencing

DOE PAGES

Trapnell, Dorset W.; Beasley, Rochelle R.; Lance, Stacey L.; ...

2015-06-05

Our premise describes how microsatellite loci were developed for the epiphytic pencil orchid Dendrobium calamiforme for population genetic and phylogeographic investigation of this Australian taxon. Nineteen microsatellite loci were identified from an Illumina paired-end shotgun library of D. calamiforme. Polymorphism and genetic diversity were assessed in 24 individuals from five populations separated by a maximum distance of ~80 km. All loci were polymorphic with two to 14 alleles per locus, expected heterozygosity ranging from 0.486 to 0.902, and probability of identity values ranging from 0.018 to 0.380. In conclusion, these novel markers will serve as valuable tools for investigation ofmore » levels of genetic diversity as well as patterns of gene flow, genetic structure, and phylogeographic history.« less

Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Gupta, Sarika; Kumari, Kajal; Sahu, Pranav Pankaj; Vidapu, Sudhakar; Prasad, Manoj

2012-02-01

The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar 'Prasad', 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F(2) mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (~74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30-0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (~18%), maize (~16%) and rice (~5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.

Alu repeats: A source for the genesis of primate microsatellites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arcot, S.S.; Batzer, M.A.; Wang, Zhenyuan

1995-09-01

As a result of their abundance, relatively uniform distribution, and high degree of polymorphism, microsatellites and minisatellites have become valuable tools in genetic mapping, forensic identity testing, and population studies. In recent years, a number of microsatellite repeats have been found to be associated with Alu interspersed repeated DNA elements. The association of an Alu element with a microsatellite repeat could result from the integration of an Alu element within a preexisting microsatellite repeat. Alternatively, Alu elements could have a direct role in the origin of microsatellite repeats. Errors introduced during reverse transcription of the primary transcript derived from anmore » Alu {open_quotes}master{close_quote} gene or the accumulation of random mutations in the middle A-rich regions and oligo(dA)-rich tails of Alu elements after insertion and subsequent expansion and contraction of these sequences could result in the genesis of a microsatellite repeat. We have tested these hypotheses by a direct evolutionary comparison of the sequences of some recent Alu elements that are found only in humans and are absent from nonhuman primates, as well as some older Alu elements that are present at orthologous positions in a number of nonhuman primates. The origin of {open_quotes}young{close_quotes} Alu insertions, absence of sequences that resemble microsatellite repeats at the orthologous loci in chimpanzees, and the gradual expansion of microsatellite repeats in some old Alu repeats at orthologous positions within the genomes of a number of nonhuman primates suggest that Alu elements are a source for the genesis of primate microsatellite repeats. 48 refs., 5 figs., 3 tabs.« less

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

USGS Publications Warehouse

Meece, J.K.; Anderson, J.L.; Fisher, M.C.; Henk, D.A.; Sloss, Brian L.; Reed, K.D.

2011-01-01

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and ??-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. ?? 2011, American Society for Microbiology.

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis based on 27 polymorphic microsatellite markers

USGS Publications Warehouse

Meece, Jennifer K.; Anderson, Jennifer L.; Fisher, Matthew C.; Henk, Daniel A.; Sloss, Brian L.; Reed, Kurt D.

2011-01-01

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.

Development and characterization of microsatellite loci for Ocotea species (Lauraceae) threatened with extinction.

PubMed

Martins, E M; Martinelli, G; Arbetman, M P; Lamont, R W; Simões-Araújo, J L; Powell, D; Ciampi-Guillardi, M; Baldauf, C; Quinet, A; Galisa, P; Shapcott, A

2014-07-07

The Atlantic rainforest species Ocotea catharinensis, Ocotea odorifera, and Ocotea porosa have been extensively harvested in the past for timber and oil extraction and are currently listed as threatened due to overexploitation. To investigate the genetic diversity and population structure of these species, we developed 8 polymorphic microsatellite markers for O. odorifera from an enriched microsatellite library by using 2 dinucleotide repeats. The microsatellite markers were tested for cross-amplification in O. catharinensis and O. porosa. The average number of alleles per locus was 10.2, considering all loci over 2 populations of O. odorifera. Observed and expected heterozygosities for O. odorifera ranged from 0.39 to 0.93 and 0.41 to 0.92 across populations, respectively. Cross-amplification of all loci was successfully observed in O. catharinensis and O. porosa except 1 locus that was found to lack polymorphism in O. porosa. Combined probabilities of identity in the studied Ocotea species were very low ranging from 1.0 x 10-24 to 7.7 x 10-24. The probability of exclusion over all loci estimated for O. odorifera indicated a 99.9% chance of correctly excluding a random nonparent individual. The microsatellite markers described in this study have high information content and will be useful for further investigations on genetic diversity within these species and for subsequent conservation purposes.

No clustering for linkage map based on low-copy and undermethylated microsatellites.

PubMed

Zhou, Yi; Gwaze, David P; Reyes-Valdés, M Humberto; Bui, Thomas; Williams, Claire G

2003-10-01

Clustering has been reported for conifer genetic maps based on hypomethylated or low-copy molecular markers, resulting in uneven marker distribution. To test this, a framework genetic map was constructed from three types of microsatellites: low-copy, undermethylated, and genomic. These Pinus taeda L. microsatellites were mapped using a three-generation pedigree with 118 progeny. The microsatellites were highly informative; of the 32 markers in intercross configuration, 29 were segregating for three or four alleles in the progeny. The sex-averaged map placed 51 of the 95 markers in 15 linkage groups at LOD > 4.0. No clustering or uneven distribution across the genome was observed. The three types of P. taeda microsatellites were randomly dispersed within each linkage group. The 51 microsatellites covered a map distance of 795 cM, an average distance of 21.8 cM between markers, roughly half of the estimated total map length. The minimum and maximum distances between any two bins was 4.4 and 45.3 cM, respectively. These microsatellites provided anchor points for framework mapping for polymorphism in P. taeda and other closely related hard pines.

Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species.

PubMed

Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M Iqbal; Zerega, Nyree J C

2013-07-01

Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

Microsatellite markers in Rhodiola (Crassulaceae), a medicinal herb genus widely used in traditional Chinese medicine.

PubMed

You, Jianling; Liu, Wensheng; Zhao, Yao; Zhu, Yongqing; Zhang, Wenju; Wang, Yuguo; Lu, Fan; Song, Zhiping

2013-03-01

Microsatellite loci are described for Rhodiola, a medicinal herb genus widely used in traditional Chinese medicine. • A total of 17 polymorphic microsatellite primer pairs were developed using the combined biotin capture method. The number of alleles per locus ranged from one to 12 across 192 individuals from R. bupleuroides, R. crenulata, R. fastigiata, and R. sacra, and the mean observed and expected heterozygosities ranged from 0.177 to 0.412 and from 0.363 to 0.578, respectively. • The results demonstrate the potential use of this new set of microsatellite markers for genotyping individuals and estimating genetic diversity in Rhodiola.

Hepatocyte Ploidy Is a Diversity Factor for Liver Homeostasis

PubMed Central

Kreutz, Clemens; MacNelly, Sabine; Follo, Marie; Wäldin, Astrid; Binninger-Lacour, Petra; Timmer, Jens; Bartolomé-Rodríguez, María M.

2017-01-01

Polyploidy, the existence of cells containing more than one pair of chromosomes, is a well-known feature of mammalian hepatocytes. Polyploid hepatocytes are found either as cells with a single polyploid nucleus or as multinucleated cells with diploid or even polyploid nuclei. In this study, we evaluate the degree of polyploidy in the murine liver by accounting both DNA content and number of nuclei per cell. We demonstrate that mouse hepatocytes with diploid nuclei have distinct metabolic characteristics compared to cells with polyploid nuclei. In addition to strong differential gene expression, comprising metabolic as well as signaling compounds, we found a strongly decreased insulin binding of nuclear polyploid cells. Our observations were associated with nuclear ploidy but not with total ploidy within a cell. We therefore suggest ploidy of the nuclei as an new diversity factor of hepatocytes and hypothesize that hepatocytes with polyploid nuclei may have distinct biological functions than mono-nuclear ones. This diversity is independent from the well-known heterogeneity related to the cells' position along the porto-central liver-axis. PMID:29163206

Isolation and Characterization of 21 Microsatellite Loci in Cardiocrinum giganteum var. yunnanense (Liliaceae), an Important Economic Plant in China

PubMed Central

Li, Rong; Yang, Jie; Yang, Junbo; Dao, Zhiling

2012-01-01

Twenty-one microsatellite markers from the genome of Cardiocrinum giganteum var. yunnanense, an important economic plant in China, were developed with a fast isolation protocol by amplified fragment length polymorphism of sequences containing repeats (FIASCO). Polymorphism within each locus was assessed in 24 wild individuals from Gaoligong Mountains in western Yunnan Province, China. The number of alleles per locus ranged from 2 to 4 with a mean of 2.9. The expected and observed levels of heterozygosity ranged from 0.042 to 0.726 and from 0.000 to 1.000, with averages of 0.44 and 0.31, respectively. These polymorphic microsatellite markers should prove useful in population genetics studies and assessments of genetic variation to develop conservation and management strategies for this species. PMID:22408400

Microsatellite in Aeschynomene falcata (Leguminosae): diversity, cross-amplification, and chromosome localization.

PubMed

Polido, C A; Mantello, C C; Moraes, A P; Souza, A P; Forni-Martins, E R

2014-12-04

Aeschynomene falcata is an important forage species; however, because of low seed production, it is underutilized as forage species. Aeschynomene is a polyphyletic genus with a challenging taxonomic position. Two subgenera have been proposed, and it is suggested that Aeschynomene can be split in 2 genera. Thus, new markers, such as microsatellite sequences, are desirable for improving breeding programs for A. falcata. Based on transferability and in situ localization, these microsatellite sequences can be applied as chromosome markers in the genus Aeschynomene and closely related genera. Here, we report the first microsatellite library developed for this genus; 11 microsatellites were characterized, with observed and expected heterozygosities ranging from 0.0000 to 0.7143 and from 0.1287 to 0.8360, respectively. Polymorphic information content varied from 0.1167 to 0.7786. The departure from Hardy-Weinberg equilibrium may have resulted from frequent autogamy, which is characteristic of A. falcata. Of the 11 microsatellites, 9 loci were cross-amplified in A. brevipes and A. paniculata and 7 in Dalbergia nigra and Machaerium vestitum. Five of these 7 cross-amplified microsatellites were applied as probes during the in situ hybridization assay and 2 showed clear signals on A. falcata chromosomes, ensuring their viability as chromosome markers.

Does the evolutionary conservation of microsatellite loci imply function?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shriver, M.D.; Deka, R.; Ferrell, R.E.

Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these fourmore » species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.« less

Mining and characterization of microsatellites from a genome of Venturia carpophila

USDA-ARS?s Scientific Manuscript database

A total of 4,021 microsatellites were mined from a genome of Venturia carpophila and 192 were selected to screen 39 isolates of the fungus collected from peach and nectarine in the southeastern USA. Of the 192 selected, 32 primers consistently and reliably produced polymorphic amplicons. Subsequentl...

The coordination of ploidy and cell size differs between cell layers in leaves

PubMed Central

Katagiri, Yohei; Hasegawa, Junko; Fujikura, Ushio; Hoshino, Rina; Matsunaga, Sachihiro; Tsukaya, Hirokazu

2016-01-01

Growth and developmental processes are occasionally accompanied by multiple rounds of DNA replication, known as endoreduplication. Coordination between endoreduplication and cell size regulation often plays a crucial role in proper organogenesis and cell differentiation. Here, we report that the level of correlation between ploidy and cell volume is different in the outer and inner cell layers of leaves of Arabidopsis thaliana using a novel imaging technique. Although there is a well-known, strong correlation between ploidy and cell volume in pavement cells of the epidermis, this correlation was extremely weak in palisade mesophyll cells. Induction of epidermis cell identity based on the expression of the homeobox gene ATML1 in mesophyll cells enhanced the level of correlation between ploidy and cell volume to near that of wild-type epidermal cells. We therefore propose that the correlation between ploidy and cell volume is regulated by cell identity. PMID:26903507

Identification and characterization of microsatellite markers in the Chagas disease vector Triatoma dimidiata

PubMed Central

Anderson, Jennifer M.; Lai, James E.; Dotson, Ellen M.; Cordon-Rosales, Celia; Ponce, Carlos; Norris, Douglas E.; Ben Beard, C.

2014-01-01

Triatoma dimidiata, one of the major vectors of Chagas disease in Central America, is found in both domestic and peri-domestic habitats. Questions concerning population boundaries, infestation rates, insecticide resistance, and geographic dispersal of triatomine bugs persist and may be resolved using genetic markers such as microsatellites. Microsatellites are short tandem repeats found dispersed throughout a genome and can be useful for genotypic identification. We developed a plasmid library from the genomic DNA isolated from a single T. dimidiata adult collected in Guatamala. Ten thousand clones were screened using a probe consisting of nine microsatellite oligonucleotides. Eight loci appear polymorphic among populations found in Guatemala, Honduras, and Mexico, and thus are potentially useful for population genetic applications. PMID:12798021

Isolation and characterization of microsatellite markers for Jasminum sambac (Oleaceae) using Illumina shotgun sequencing1

PubMed Central

Li, Yong; Zhang, Weirui

2015-01-01

Premise of the study: Microsatellite markers of Jasminum sambac (Oleaceae) were isolated to investigate wild germplasm resources and provide markers for breeding. Methods and Results: Illumina sequencing was used to isolate microsatellite markers from the transcriptome of J. sambac. A total of 1322 microsatellites were identified from 49,772 assembled unigenes. One hundred primer pairs were randomly selected to verify primer amplification efficiency. Out of these tested primer pairs, 31 were successfully amplified: 18 primer pairs yielded a single allele, seven exhibited fixed heterozygosity with two alleles, and only six displayed polymorphisms. Conclusions: This study obtained the first set of microsatellite markers for J. sambac, which will be helpful for the assessment of wild germplasm resources and the development of molecular marker–assisted breeding. PMID:26504683

Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus

PubMed Central

Fonseca, Paulo J.; Amorim, Maria Clara P.

2015-01-01

The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy–Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species. PMID:25653909

Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis)

USGS Publications Warehouse

Ramey, A.; Graziano, S.L.; Nielsen, J.L.

2008-01-01

Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco. ?? 2007 Blackwell Publishing Ltd.

Isolation and characterization of microsatellite loci in an endangered tree species, Afzelia xylocarpa (Kurz) Craib (Caesalpinioideae).

PubMed

Pakkad, Greuk; Ueno, Saneyoshi; Yoshimaru, Hiroshi

2009-05-01

Afzelia xylocarpa is listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources World list of Threatened Trees, due to overexploitation for its valuable timber and habitat loss. We isolated eight polymorphic microsatellite loci from A. xylocarpa using dual suppression polymerase chain reaction technique. These loci provide microsatellite markers with high polymorphism, as the number of alleles ranged from two to seven, and the estimate of gene diversity was between 0.285 and 0.795. The markers are now available for more detailed investigation of population genetic structure and gene flow among A. xylocarpa populations. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.)

PubMed Central

Ritschel, Patricia Silva; Lins, Tulio Cesar de Lima; Tristan, Rodrigo Lourenço; Buso, Gláucia Salles Cortopassi; Buso, José Amauri; Ferreira, Márcio Elias

2004-01-01

Background Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species. Results Seven hundred clones containing microsatellite sequences from a Tsp-AG/TC microsatellite enriched library were identified and one-hundred and forty-four primer pairs designed and synthesized. When 67 microsatellite markers were tested on a panel of melon and other cucurbit accessions, 65 revealed DNA polymorphisms among the melon accessions. For some cucurbit species, such as Cucumis sativus, up to 50% of the melon microsatellite markers could be readily used for DNA polymophism assessment, representing a significant reduction of marker development costs. A random sample of 25 microsatellite markers was extracted from the new microsatellite marker set and characterized on 40 accessions of melon, generating an allelic frequency database for the species. The average expected heterozygosity was 0.52, varying from 0.45 to 0.70, indicating that a small set of selected markers should be sufficient to solve questions regarding genotype identity and variety protection. Genetic distances based on microsatellite polymorphism were congruent with data obtained from RAPD marker analysis. Mapping analysis was initiated with 55 newly developed markers and most primers showed segregation according to Mendelian expectations. Linkage analysis detected linkage between 56% of the markers, distributed in nine linkage groups. Conclusions Genomic library microsatellite enrichment is an efficient procedure for marker

Characterization of microsatellite loci isolated in Mountain Plover (Charadrius montanus)

USGS Publications Warehouse

John, J. St; Kysela, R.F.; Oyler-McCance, S.J.

2007-01-01

Primers for 15 microsatellite loci were developed for Mountain Plover, a species whose distribution and abundance have been reduced drastically in the past 30 years. In a screen of 126 individuals collected from four breeding locales across the species' range, levels of polymorphism ranged from two to 13 alleles per locus. No two loci were found to be linked, although one locus revealed significant departures from Hardy-Weinberg equilibrium. These microsatellite loci can be used in population genetic studies, ultimately aiding in management efforts for Mountain Plover. Additionally, these markers can potentially be used in studies investigating the mating system of Mountain Plover. ?? 2007 Blackwell Publishing Ltd.

Characterization of microsatellite loci for an Australian epiphytic orchid, Dendrobium calamiforme, using Illumina sequencing1

PubMed Central

Trapnell, Dorset W.; Beasley, Rochelle R.; Lance, Stacey L.; Field, Ashley R.; Jones, Kenneth L.

2015-01-01

Premise of the study: Microsatellite loci were developed for the epiphytic pencil orchid Dendrobium calamiforme for population genetic and phylogeographic investigation of this Australian taxon. Methods and Results: Nineteen microsatellite loci were identified from an Illumina paired-end shotgun library of D. calamiforme. Polymorphism and genetic diversity were assessed in 24 individuals from five populations separated by a maximum distance of ∼80 km. All loci were polymorphic with two to 14 alleles per locus, expected heterozygosity ranging from 0.486 to 0.902, and probability of identity values ranging from 0.018 to 0.380. Conclusions: These novel markers will serve as valuable tools for investigation of levels of genetic diversity as well as patterns of gene flow, genetic structure, and phylogeographic history. PMID:26082878

Development and characterization of microsatellite loci in the mistletoe Psittacanthus schiedeanus (Loranthaceae)1

PubMed Central

González, Clementina; Harvey, Nick; Ornelas, Juan Francisco

2015-01-01

• Premise of the study: Microsatellite primers were developed for the parasitic Psittacanthus schiedeanus, a common mistletoe species on cloud forest–adapted tree hosts in Mesoamerica, to investigate intraspecific genetic patterns of diversity and genetic structure. • Methods and Results: Using an enriched library, 10 polymorphic microsatellite loci were developed in P. schiedeanus. All loci consisted of dinucleotide repeats. Average alleles per locus were 12 (4–17), and a total of 120 alleles were recorded across 39 individuals from four populations in Mexico. Primers were tested in 11 additional species, but only amplified successfully in P. calyculatus and P. angustifolius. • Conclusions: The polymorphic loci described will be useful in studies of genetic diversity and genetic population differentiation in natural populations of these parasitic plants, and will provide valuable information to understand the importance of host distribution. PMID:25606357

Fast and Cost-Effective Mining of Microsatellite Markers Using NGS Technology: An Example of a Korean Water Deer Hydropotes inermis argyropus

PubMed Central

Yu, Jeong-Nam; Won, Changman; Jun, Jumin; Lim, YoungWoon; Kwak, Myounghai

2011-01-01

Background Microsatellites, a special class of repetitive DNA sequence, have become one of the most popular genetic markers for population/conservation genetic studies. However, its application to endangered species has been impeded by high development costs, a lack of available sequences, and technical difficulties. The water deer Hydropotes inermis is the sole existing endangered species of the subfamily Capreolinae. Although population genetics studies are urgently required for conservation management, no species-specific microsatellite marker has been reported. Methods We adopted next-generation sequencing (NGS) to elucidate the microsatellite markers of Korean water deer and overcome these impediments on marker developments. We performed genotyping to determine the efficiency of this method as applied to population genetics. Results We obtained 98 Mbp of nucleotide information from 260,467 sequence reads. A total of 20,101 di-/tri-nucleotide repeat motifs were identified; di-repeats were 5.9-fold more common than tri-repeats. [CA]n and [AAC]n/[AAT]n repeats were the most frequent di- and tri-repeats, respectively. Of the 17,206 di-repeats, 12,471 microsatellite primer pairs were derived. PCR amplification of 400 primer pairs yielded 106 amplicons and 79 polymorphic markers from 20 individual Korean water deer. Polymorphic rates of the 79 new microsatellites varied from 2 to 11 alleles per locus (He: 0.050–0.880; Ho: 0.000–1.000), while those of known microsatellite markers transferred from cattle to Chinese water deer ranged from 4 to 6 alleles per locus (He: 0.279–0.714; Ho: 0.300–0.400). Conclusions Polymorphic microsatellite markers from Korean water deer were successfully identified using NGS without any prior sequence information and deposited into the public database. Thus, the methods described herein represent a rapid and low-cost way to investigate the population genetics of endangered/non-model species. PMID:22069476

PCR primers for microsatellite loci in the desert tortoise (Gopherus agassizii, Testudinidae)

USGS Publications Warehouse

Edwards, T.; Goldberg, C.S.; Kaplan, M.E.; Schwalbe, C.R.; Swann, D.E.

2003-01-01

The desert tortoise, Gopherus agassizii, is a threatened species native to the North American desert southwest and is recognized as having distinct Mojave and Sonoran populations. We identified six polymorphic microsatellite loci in the desert tortoise. All six loci were polymorphic in Sonoran samples. Five of the loci were variable in Mojave samples with varying degrees of amplification success. Two of the loci exhibited low allelic variation (2-3 alleles) while four were highly variable (8-27 alleles).

Isolation and characterization of microsatellite markers for carolina hemlock (Tsuga caroliniana)

Treesearch

S.A. Josserand; K.M. Potter; C.S. Echt; C.D. Nelson

2008-01-01

We describe the isolation and characterization of 31 polymorphic di- and trinucleotide microsatellite marker loci for Carolina hemlock (Tsuga caroliniana Englem.). In addition, primer pairs for 16 loci amplified scoreable alleles in six other Euga species. In eastern North America, both Carolina hemlock and eastern hemlock (Tsuga canadensis...

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.

PubMed Central

2014-01-01

Background Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species. Result A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective. Conclusions A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species. PMID:24472631

The coordination of ploidy and cell size differs between cell layers in leaves.

PubMed

Katagiri, Yohei; Hasegawa, Junko; Fujikura, Ushio; Hoshino, Rina; Matsunaga, Sachihiro; Tsukaya, Hirokazu

2016-04-01

Growth and developmental processes are occasionally accompanied by multiple rounds of DNA replication, known as endoreduplication. Coordination between endoreduplication and cell size regulation often plays a crucial role in proper organogenesis and cell differentiation. Here, we report that the level of correlation between ploidy and cell volume is different in the outer and inner cell layers of leaves of Arabidopsis thaliana using a novel imaging technique. Although there is a well-known, strong correlation between ploidy and cell volume in pavement cells of the epidermis, this correlation was extremely weak in palisade mesophyll cells. Induction of epidermis cell identity based on the expression of the homeobox gene ATML1 in mesophyll cells enhanced the level of correlation between ploidy and cell volume to near that of wild-type epidermal cells. We therefore propose that the correlation between ploidy and cell volume is regulated by cell identity. © 2016. Published by The Company of Biologists Ltd.

The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion.

PubMed

Sing, Tina L; Hung, Minnie P; Ohnuki, Shinsuke; Suzuki, Godai; San Luis, Bryan-Joseph; McClain, Melainia; Unruh, Jay R; Yu, Zulin; Ou, Jiongwen; Marshall-Sheppard, Jesse; Huh, Won-Ki; Costanzo, Michael; Boone, Charles; Ohya, Yoshikazu; Jaspersen, Sue L; Brown, Grant W

2018-06-06

Ploidy is tightly regulated in eukaryotic cells and is critical for cell function and survival. Cells coordinate multiple pathways to ensure replicated DNA is segregated accurately to prevent abnormal changes in chromosome number. In this study, we characterize an unanticipated role for the Saccharomyces cerevisiae "remodels the structure of chromatin" (RSC) complex in ploidy maintenance. We show that deletion of any of six nonessential RSC genes causes a rapid transition from haploid to diploid DNA content because of nondisjunction events. Diploidization is accompanied by diagnostic changes in cell morphology and is stably maintained without further ploidy increases. We find that RSC promotes chromosome segregation by facilitating spindle pole body (SPB) duplication. More specifically, RSC plays a role in distributing two SPB insertion factors, Nbp1 and Ndc1, to the new SPB. Thus, we provide insight into a role for a SWI/SNF family complex in SPB duplication and ploidy maintenance. © 2018 Sing et al.

Novel microsatellite development and characterization for Phacelia formosula (Hydrophyllaceae)1

PubMed Central

Schwabe, Anna L.; Neale, Jennifer Ramp

2017-01-01

Premise of the study: Microsatellite primers were developed to characterize genetic diversity and structuring in the genus Phacelia (Hydrophyllaceae) and to further conservation efforts for P. formosula. Methods and Results: Fifteen novel microsatellite primers were developed for P. formosula. These were characterized for genetic variation in three separate P. formosula populations. Two to nine alleles were found per locus. Overall observed heterozygosity and expected heterozygosity ranged from 0.000 to 0.800 and 0.000 to 0.840, respectively. Additionally, these loci were successfully amplified and showed polymorphism in P. gina-glenneae and a potential new Phacelia species. Conclusions: These microsatellite markers will be useful in assessing genetic diversity, structuring, and gene flow within and among populations of the rare P. formosula, in addition to related Phacelia species. These markers will provide important genetic data needed for appropriate conservation and management of these rare plants. PMID:28791208

Tracing Asian Seabass Individuals to Single Fish Farms Using Microsatellites

PubMed Central

Yue, Gen Hua; Xia, Jun Hong; Liu, Peng; Liu, Feng; Sun, Fei; Lin, Grace

2012-01-01

Traceability through physical labels is well established, but it is not highly reliable as physical labels can be easily changed or lost. Application of DNA markers to the traceability of food plays an increasingly important role for consumer protection and confidence building. In this study, we tested the efficiency of 16 polymorphic microsatellites and their combinations for tracing 368 fish to four populations where they originated. Using the maximum likelihood and Bayesian methods, three most efficient microsatellites were required to assign over 95% of fish to the correct populations. Selection of markers based on the assignment score estimated with the software WHICHLOCI was most effective in choosing markers for individual assignment, followed by the selection based on the allele number of individual markers. By combining rapid DNA extraction, and high-throughput genotyping of selected microsatellites, it is possible to conduct routine genetic traceability with high accuracy in Asian seabass. PMID:23285169

Identification and characterization of microsatellite loci in two socially complex old world tropical babblers (Family Timaliidae).

PubMed

Kaiser, Sara A; Danner, J E; Bergner, Laura; Fleischer, Robert C

2015-11-24

Although the highest diversity of birds occurs in tropical regions, little is known about the genetic mating systems of most tropical species. We describe microsatellite markers isolated in the chestnut-crested yuhina (Staphida everetti), endemic to the island of Borneo, and the grey-throated babbler (Stachyris nigriceps), widely distributed across Southeast Asia. Both species belong to the avian family Timaliidae and are highly social, putatively cooperatively breeding birds in which helpers attend the nests of members of their social group. We obtained DNA from individuals in social groups breeding in Kinabalu Park, Malaysian Borneo. We used a shotgun sequencing approach and 454-technology to identify 36 microsatellite loci in the yuhina and 40 in the babbler. We tested 13 primer pairs in yuhinas and 20 in babblers and characterized eight polymorphic loci in 20 unrelated female yuhinas and 21 unrelated female babblers. Polymorphism at the yuhina loci ranged from 3 to 9 alleles, observed heterozygosities from 0.58 to 1.00, and expected heterozygosities from 0.64 to 0.81. Polymorphism at the babbler loci ranged from 3 to 12 alleles, observed heterozygosities from 0.14 to 0.90 and expected heterozygosities from 0.14 to 0.87. One locus in the yuhina deviated significantly from Hardy-Weinberg equilibrium. We detected nonrandom allele associations between two pairs of microsatellite loci in each species. Microsatellite markers will be used to describe the genetic mating system of these socially complex species and to measure genetic parentage and relatedness within social groups.

Development of multiplex microsatellite PCR panels for the seagrass Thalassia hemprichii (Hydrocharitaceae).

PubMed

van Dijk, Kor-Jent; Mellors, Jane; Waycott, Michelle

2014-11-01

New microsatellites were developed for the seagrass Thalassia hemprichii (Hydrocharitaceae), a long-lived seagrass species that is found throughout the shallow waters of tropical and subtropical Indo-West Pacific. Three multiplex PCR panels were designed utilizing new and previously developed markers, resulting in a toolkit for generating a 16-locus genotype. • Through the use of microsatellite enrichment and next-generation sequencing, 16 new, validated, polymorphic microsatellite markers were isolated. Diversity was between two and four alleles per locus totaling 36 alleles. These markers, plus previously developed microsatellite markers for T. hemprichii and T. testudinum, were tested for suitability in multiplex PCR panels. • The generation of an easily replicated suite of multiplex panels of codominant molecular markers will allow for high-resolution and detailed genetic structure analysis and clonality assessment with minimal genotyping costs. We suggest the establishment of a T. hemprichii primer convention for the unification of future data sets.

Genetic characterization of commercial honey bee (Hymenoptera: Apidae) populations in the United States by using mitochondrial and microsatellite markers

Treesearch

D. A. Delaney; M.D. Meixner; N.M. Schiff; W.S. Sheppard

2009-01-01

Genetic diversity levels within and between the two commercial breeding areas in theUnited States were analyzed using the DraI restriction fragment length polymorphism of the COICOII mitochondrial region and 10 polymorphic microsatellite loci. The western commercial breeding population (WCBP) and the southeastern commercial...

Comparative study on the use of specific and heterologous microsatellite primers in the stingless bees Melipona rufiventris and M. mondury (Hymenoptera, Apidae).

PubMed

Lopes, Denilce Meneses; de Oliveira Campos, Lúcio Antônio; Salomão, Tânia Maria Fernandes; Tavares, Mara Garcia

2010-04-01

Due to their high degree of polymorphism, microsatellites are considered useful tools for studying population genetics. Nevertheless, studies of genetic diversity in stingless bees by means of these primers have revealed a low level of polymorphism, possibly the consequence of the heterologous primers used, since in most cases these were not specifically designed for the species under consideration. Herein we compared the number of polymorphic loci and alleles per locus, as well as observed heterozygosity in Melipona rufiventris and M. mondury populations, using specific and heterologous primers. The use of specific primers placed in evidence the greater frequency of polymorphic loci and alleles per locus, besides an expressive increase in observed heterozygosity in M. rufiventris and M. mondury, thereby reinforcing the idea that populational studies should be undertaken by preferably using species-specific microsatellite primers.

Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Sorcidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus

USGS Publications Warehouse

Sonsthagen, Sarah A.; Sage, G. Kevin; Fowler, Megan C.; Hope, Andrew G.; Cook, J.A.; Talbot, Sandra L.

2013-01-01

We used next generation shotgun sequencing to develop 21 novel microsatellite markers for the barren-ground shrew (Sorex ugyunak), which were polymorphic among individuals from northern Alaska. The loci displayed moderate allelic diversity (averaging 6.81 alleles per locus) and heterozygosity (averaging 70 %). Two loci deviated from Hardy–Weinberg equilibrium (HWE) due to heterozygote deficiency. While the population did not deviate from HWE overall, it showed significant linkage disequilibrium suggesting this population is not in mutation-drift equilibrium. Nineteen of 21 loci were polymorphic in masked shrews (S. cinereus) from interior Alaska and exhibited linkage equilibrium and HWE overall. All loci yielded sufficient variability for use in population studies.

Microsatellite loci in Vallisneria natans (Hydrocharitaceae) and cross-reactivity with V. spinulosa and V. denseserrulata.

PubMed

Wang, Bin; Liao, Hui; Zhao, Yao; Li, Wei; Song, Zhiping

2011-03-01

Microsatellite primers were characterized in Vallisneria natans, a dominant submerged macrophyte occurring in freshwater bodies of tropical and subtropical zones. Using the Microsatellite Sequence Enrichment protocol, 16 novel polymorphic codominant loci were developed and characterized in V. natans. In addition to these, six existing microsatellite loci from V. spinulosa were successfully amplified and characterized for V. natans. These primers amplified di- and trinucleotide repeats with 2-7 alleles per locus. Most primers also amplified successfully in V. spinulosa and V. denseserrulata. These results indicate the utility of primers in V. natans for future studies of population genetic structure, as well as their applicability across the genus.

Characterization of polymorphic microsatellites for Tripterygium (Celastraceae), a monospecific genus of medicinal importance.

PubMed

Novy, Ari; Jones, Kenneth C

2011-10-01

Microsatellite markers were developed for the medicinal plant Tripterygium (Celastraceae) to assess its population structure and to facilitate source tracking of plant materials used for medicinal extracts. Ten microsatellite markers were isolated and characterized in T. wilfordii using an enriched genomic library. The number of alleles per locus ranged from five to 12. Observed and expected heterozygosity ranged from 0.166 to 0.630 and 0.392 to 0.562, respectively. These markers will be useful for a variety of applications including source tracking of plant materials, resolution of taxonomic issues, and population genetics studies.

Development and characterization of microsatellite loci in the endangered species Taxus wallichiana (Taxaceae).

PubMed

Gajurel, Jyoti Prasad; Cornejo, Carolina; Werth, Silke; Shrestha, Krishna Kumar; Scheidegger, Christoph

2013-03-01

Microsatellite primers were developed in the endangered tree species Taxus wallichiana from Nepal to investigate regional genetic differentiation, local genetic diversity, and gene flow for the conservation of this species under climate- and land-use change scenarios in mountain regions of Nepal. • We developed 10 highly polymorphic microsatellite markers from 454 DNA sequencing. Characterization of the new microsatellite loci was done in 99 individuals collected from three valleys with different climatic regimes. The number of alleles per locus varied from four to 12. Observed heterozygosity of populations, averaged across loci, ranged from 0.30 to 0.59. • The new markers provided by this study will substantially increase the resolution for detailed studies in phylogeography, population genetics, and parentage analysis.

Economic evaluation of DNA ploidy analysis vs liquid-based cytology for cervical screening.

PubMed

Nghiem, V T; Davies, K R; Beck, J R; Follen, M; MacAulay, C; Guillaud, M; Cantor, S B

2015-06-09

DNA ploidy analysis involves automated quantification of chromosomal aneuploidy, a potential marker of progression toward cervical carcinoma. We evaluated the cost-effectiveness of this method for cervical screening, comparing five ploidy strategies (using different numbers of aneuploid cells as cut points) with liquid-based Papanicolaou smear and no screening. A state-transition Markov model simulated the natural history of HPV infection and possible progression into cervical neoplasia in a cohort of 12-year-old females. The analysis evaluated cost in 2012 US$ and effectiveness in quality-adjusted life-years (QALYs) from a health-system perspective throughout a lifetime horizon in the US setting. We calculated incremental cost-effectiveness ratios (ICERs) to determine the best strategy. The robustness of optimal choices was examined in deterministic and probabilistic sensitivity analyses. In the base-case analysis, the ploidy 4 cell strategy was cost-effective, yielding an increase of 0.032 QALY and an ICER of $18 264/QALY compared to no screening. For most scenarios in the deterministic sensitivity analysis, the ploidy 4 cell strategy was the only cost-effective strategy. Cost-effectiveness acceptability curves showed that this strategy was more likely to be cost-effective than the Papanicolaou smear. Compared to the liquid-based Papanicolaou smear, screening with a DNA ploidy strategy appeared less costly and comparably effective.

Characterization of Novel Di-, Tri-, and Tetranucleotide Microsatellite Primers Suitable for Genotyping Various Plant Pathogenic Fungi with Special Emphasis on Fusaria and Mycospherella graminicola

PubMed Central

Bahkali, Ali H.; Abd-Elsalam, Kamel A.; Guo, Jian-Rong; Khiyami, Mohamed A.; Verreet, Joseph-Alexander

2012-01-01

The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM) analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence of Mycospherlla graminicola and Fusarium graminearum. A total of 20 new microsatellite primers as easy-to-score markers were developed. Microsatellite primer PCR (MP-PCR) yielded highly reproducible and complex genomic fingerprints, with several bands ranging in size from 200 to 3000 bp. Of the 20 primers tested, only (TAGG)4, (TCC)5 and (CA)7T produced a high number of polymorphic bands from either F. graminearum or F. culmorum. (ATG)5 led to successful amplifications in M. graminicola isolates collected from Germany. Percentage of polymorphic bands among Fusarium species ranged from 9 to 100%. Cluster analysis of banding patterns of the isolates corresponded well to the established species delineations based on morphology and other methods of phylogenetic analysis. The current research demonstrates that the newly designed microsatellite primers are reliable, sensitive and technically simple tools for assaying genetic variability in plant pathogenic fungi. PMID:22489135

Prognostic importance of DNA ploidy in non-endometrioid, high-risk endometrial carcinomas.

PubMed

Sorbe, Bengt

2016-03-01

The present study investigated the predictive and prognostic impact of DNA ploidy together with other well-known prognostic factors in a series of non-endometrioid, high-risk endometrial carcinomas. From a complete consecutive series of 4,543 endometrial carcinomas of International Federation of Gynecology and Obstetrics (FIGO) stages I-IV, 94 serous carcinomas, 48 clear cell carcinomas and 231 carcinosarcomas were selected as a non-endometrioid, high-risk group for further studies regarding prognosis. The impact of DNA ploidy, as assessed by flow cytometry, was of particular focus. The age of the patients, FIGO stage, depth of myometrial infiltration and tumor expression of p53 were also included in the analyses (univariate and multivariate). In the complete series of cases, the recurrence rate was 37%, and the 5-year overall survival rate was 39% with no difference between the three histological subtypes. The primary cure rate (78%) was also similar for all tumor types studied. DNA ploidy was a significant predictive factor (on univariate analysis) for primary tumor cure rate, and a prognostic factor for survival rate (on univariate and multivariate analyses). The predictive and prognostic impact of DNA ploidy was higher in carcinosarcomas than in serous and clear cell carcinomas. In the majority of multivariate analyses, FIGO stage and depth of myometrial infiltration were the most important predictive (tumor recurrence) and prognostic (survival rate) factors. DNA ploidy status is a less important predictive and prognostic factor in non-endometrioid, high-risk endometrial carcinomas than in the common endometrioid carcinomas, in which FIGO and nuclear grade also are highly significant and important factors.

Polymorphism of Glucokinase Gene in Non-Insulin Dependent Diabetes Mellitus

PubMed Central

Kim, Deog-Yoon; Choi, Jung-Hee; Woo, Jeong-Taek; Paeng, Jeong-Ryung; Yang, In-Myung; Kim, Sung-Woon; Kim, Jin-Woo; Kim, Young-Seol; Kim, Kwang-Won; Choi, Young-Kil

1994-01-01

Several lines of evidence suggest a strong genetic component to NIDDM. To clarify the role of glucokinase gene in the development of NIDDM, restriction fragment length polymorphism (RFLP) of glucokinase gene and 3′ microsatellite polymorphism analyses by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) were performed in NIDDM and control subjects. Compared to NIDDM with 1.3 kb allele/Pvu I digestion of glucokinase, 10% of NIDDM did not demonstrate 1.3 kb allele and these patients were charcterized by increased insulin secretion. In 3′ microsatellite polymorphism analysis, autoradiography of PCR products revealed three different alleles, including Z, Z+2 and Z+4. Z was the most common allele in both NIDDM and nondiabetic controls. There was no significant allele associated with NIDDM. Frequency of the homozygote Z/Z genotype was significantly lower in NIDDM subjects (16.7%) compared to normal control (46.7%) (p<0.05). There was no difference in clinical findings according to 3′ microsatellite genotypes in NIDDM. These data suggest that there does not appear to be a significant glucokinase allele associated with NIDDM but Z/Z genotype may play a suppressive role in the pathogenesis of a certain type of NIDDM in Korea. Further studies may be required to identify the molecular basis of this association. PMID:7913622

Isolation and characterization of microsatellite loci for mountain mullet (Agonostomus monticola).

PubMed

Feldheim, Kevin A; Sanchez, Patrick J; Matamoros, Wilfredo A; Schaefer, Jacob F; Kreiser, Brian R

2009-11-01

We report on the isolation of 15 polymorphic microsatellite loci from mountain mullet (Agonostomus monticola). In the two populations sampled, loci exhibited two to 21 alleles and observed heterozygosity values ranged from 0.222 to 1.000. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Although A. monticola is an important subsistence fishery in parts of its range, little is known about its ecology and many populations appear to be experiencing declines. These microsatellite loci should prove useful in the study of population structure of A. monticola and aid in other potential conservation efforts such as the management of hatchery broodstock. © 2009 Blackwell Publishing Ltd.

Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species1

PubMed Central

Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M. Iqbal; Zerega, Nyree J. C.

2013-01-01

• Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit. PMID:25202565

Isolation and characterization of 108 novel microsatellite loci for Atlantic coastal killifish (Fundulus heteroclitus)

EPA Science Inventory

We characterized 108 polymorphic microsatellite loci for the mummichog (Fundulus heteroclitus), an Atlantic coastal killifish. Allelic diversity among 26 individuals ranged between 2 and 15 alleles per locus, while expected heterozygosity ranged from 0.075 to 0.904. Significant ...

Comparative study on the use of specific and heterologous microsatellite primers in the stingless bees Melipona rufiventris and M. mondury (Hymenoptera, Apidae)

PubMed Central

2010-01-01

Due to their high degree of polymorphism, microsatellites are considered useful tools for studying population genetics. Nevertheless, studies of genetic diversity in stingless bees by means of these primers have revealed a low level of polymorphism, possibly the consequence of the heterologous primers used, since in most cases these were not specifically designed for the species under consideration. Herein we compared the number of polymorphic loci and alleles per locus, as well as observed heterozygosity in Melipona rufiventris and M. mondury populations, using specific and heterologous primers. The use of specific primers placed in evidence the greater frequency of polymorphic loci and alleles per locus, besides an expressive increase in observed heterozygosity in M. rufiventris and M. mondury, thereby reinforcing the idea that populational studies should be undertaken by preferably using species-specific microsatellite primers. PMID:21637499

The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

PubMed

Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

2015-01-01

Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

Development of multiplex microsatellite PCR panels for the seagrass Thalassia hemprichii (Hydrocharitaceae)1

PubMed Central

van Dijk, Kor-jent; Mellors, Jane; Waycott, Michelle

2014-01-01

• Premise of the study: New microsatellites were developed for the seagrass Thalassia hemprichii (Hydrocharitaceae), a long-lived seagrass species that is found throughout the shallow waters of tropical and subtropical Indo-West Pacific. Three multiplex PCR panels were designed utilizing new and previously developed markers, resulting in a toolkit for generating a 16-locus genotype. • Methods and Results: Through the use of microsatellite enrichment and next-generation sequencing, 16 new, validated, polymorphic microsatellite markers were isolated. Diversity was between two and four alleles per locus totaling 36 alleles. These markers, plus previously developed microsatellite markers for T. hemprichii and T. testudinum, were tested for suitability in multiplex PCR panels. • Conclusions: The generation of an easily replicated suite of multiplex panels of codominant molecular markers will allow for high-resolution and detailed genetic structure analysis and clonality assessment with minimal genotyping costs. We suggest the establishment of a T. hemprichii primer convention for the unification of future data sets. PMID:25383269

Development of microsatellites from Fothergilla ×intermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae1

PubMed Central

Hatmaker, E. Anne; Wadl, Phillip A.; Mantooth, Kristie; Scheffler, Brian E.; Ownley, Bonnie H.; Trigiano, Robert N.

2015-01-01

Premise of the study: We developed microsatellites from Fothergilla ×intermedia to establish loci capable of distinguishing species and cultivars, and to assess genetic diversity for use by ornamental breeders and to transfer within Hamamelidaceae. Methods and Results: We sequenced a small insert genomic library enriched for microsatellites to develop 12 polymorphic microsatellite loci. The number of alleles detected ranged from four to 15 across five genera within Hamamelidaceae. Shannon’s information index ranged from 0.07 to 0.14. Conclusions: These microsatellite loci provide a set of markers to evaluate genetic diversity of natural and cultivated collections and assist ornamental plant breeders for genetic studies of five popular genera of woody ornamental plants. PMID:25909044

Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca).

PubMed

Song, Xuhao; Shen, Fujun; Huang, Jie; Huang, Yan; Du, Lianming; Wang, Chengdong; Fan, Zhenxin; Hou, Rong; Yue, Bisong; Zhang, Xiuyue

2016-09-01

Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microsatellite Imputation for parental verification from SNP across multiple Bos taurus and indicus breeds

USDA-ARS?s Scientific Manuscript database

Microsatellite markers (MS) have traditionally been used for parental verification and are still the international standard in spite of their higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP)-based assays. Despite domestic and international demands fro...

Heterologous amplification and characterization of microsatellite markers in the Neotropical fish Leporinus friderici.

PubMed

Olivatti, A M; Boni, T A; Silva-Júnior, N J; Resende, L V; Gouveia, F O; Telles, M P C

2011-01-01

Leporinus friderici, native to the Amazon Basin and popularly known as "piau-três-pintas", has great ecological and economic importance; it is widely fished and consumed throughout much of tropical South America. Knowledge of the genetic diversity of this native species is important to support management and conservation programs. We evaluated microsatellite loci amplification, using heterologous primers, in 31 individuals of L. friderici. These samples were collected from natural populations of the Araguaia River basin, in central Brazil, and the DNA was extracted from samples of muscle tissue. Eight loci were successfully analyzed. Six of them were polymorphic, and the number of alleles ranged from three to 10. Values of expected heterozygosities for these polymorphic loci ranged from 0.488 to 0.795. Exclusion probability (0.983), the identity probability (0.000073), and the mean genetic diversity values were high, showing that these microsatellite markers are suitable for assessing the genetic variability of L. friderici populations. There is a growing interest in studies that evaluate the genetic variability of natural populations for various purposes, such as conservation. Here, we showed that a viable alternative to the costly development of specific primers for fish populations is simply testing for heterologous amplification of microsatellite markers available from research on other species.

Development of novel microsatellite markers for the Northern Goshawk (Accipiter gentilis) and their utility in cross-species amplification

USGS Publications Warehouse

Haughey, Christy; Sage, George K.; Degange, Gabriel; Sonsthagen, Sarah A.; Talbot, Sandra L.

2016-01-01

The Northern Goshawk (Accipiter gentilis) is a large forest raptor with a Holarctic distribution and, in some portions of its range, a species of conservation concern. To augment previously reported genetic markers, 13 novel polymorphic microsatellite markers were developed to establish individual identification and familial relationships, to assess levels of genetic diversity, and to identify diagnostic markers. Of the 22 loci tested, 13 were polymorphic, seven were monomorphic, and two failed to amplify. This suite of microsatellite loci yielded a combined probability of parental exclusion of 98%; a single individual sampled from a North American population can be reliably identified using a combination of seven of the 13 polymorphic loci. Cross-species screening in Cooper's Hawks (A. cooperii) and Sharp-shinned Hawks (A. striatus) of the 20 loci that successfully amplified in Northern Goshawks identified 13 loci as polymorphic in each species. Six of these loci (Age1303, Age1308, Age1309, Age1312, and Age1314) appeared to be useful in distinguishing between Accipiter species. These markers will be useful to researchers investigating populations of North American accipiters.

A comparative genetic analysis of the Irish greyhound population using multilocus DNA fingerprinting, canine single locus minisatellites and canine microsatellites.

PubMed

Sutton, M D; Holmes, N G; Brennan, F B; Binns, M M; Kelly, E P; Duke, E J

1998-06-01

Pairwise analysis of HinfI/33.6 DNA fingerprints from a total of one hundred and fifty-three Irish greyhounds of known pedigree were used to determine band-share estimates of unrelated, first-degree and second-degree relationships. Forty-eight unrelated Irish greyhounds were used to determine allele frequencies for three single-locus minisatellites, and following a preliminary screen, eight of the most polymorphic tetra-nucleotide microsatellites from a panel of 15. The results indicated that both band-share estimates by DNA fingerprinting and microsatellite allele frequencies are highly effective in resolving parentage in this greyhound population, while single-locus minisatellites showed limited polymorphism and could not be used alone for routine parentage testing in this breed. The present study also demonstrated that, to obtain optimal resolution of parentage, sample sets of known pedigree status are required to determine the band-share distribution and/or microsatellite allele frequencies.

[Study on association of CTLA4 gene polymorphism with Grave's disease in Guangxi Zhuang nationality population].

PubMed

Liang, Xing-huan; Qin, Ying-fen; Ma, Yan; Xie, Xin-rong; Xie, Kai-qing; Luo, Zuo-jie

2006-06-01

To investigate the relationship between the polymorphic (AT)n repeats in 3ountranslated region of exon 4 of CTLA4 gene [CTLA4(AT)n] and Graveso disease (GD) in Zhuang nationality population of Guangxi province. The studied groups comprised 48 patients with GD and 44 normal controls. Amplification of target DNA was carried out by polymerase chain reaction (PCR). The amplified products were run by 8% polyacrylamide gel electrophoresis, and then followed by 0.1% silver staining. Some of amplified products were sequenced directly. Nineteen alleles of CTLA4 gene microsatellite polymorphism were found in Guangxi Zhuang nationality individuals. The 106 bp long allele was apparently increased in patients with GD of Zhuang nationality but not in healthy controls (P< 0.05). CTLA4 gene microsatellite polymorphism is strongly associated with Graveso disease in Zhuang nationality population of Guangxi province. CTLA4(AT)n 106 bp may be the susceptible gene in GD patients of Zhuang nationality in Guangxi; 19 alleles of CTLA4 gene microsatellite polymorphism were found in Guangxi Zhuang nationality individuals.

Genetic Polymorphisms of TLR4 and MICA are Associated with Severity of Trachoma Disease in Tanzania

PubMed Central

Abbas, Muneer; Berka, Noureddine; Khraiwesh, Mozna; Ramadan, Ali; Apprey, Victor; Furbert-Harris, Paulette; Quinn, Thomas; Brim, Hassan; Dunston, Georgia

2016-01-01

Aim To examine the association of TLR4 Asp299Gly and MICA exon 5 microsatellites polymorphisms with severity of trachoma in a sub-Saharan East Africa population of Tanzanian villagers. Methods The samples were genotyped for MICA exon 5 microsatellites and the TLR4 299 A/G polymorphism by Restriction Fragment Length Polymorphism (RFLP), and GeneScan®, respectively. The association of TLR4 Asp299Gly and MICA exon 5 microsatellites with inflammatory trachoma (TI) and trichiasis (TI) were examined. Results The results showed an association between TLR4 and MICA polymorphisms and trachoma disease severity, as well as with protection. TLR4 an allele was significantly associated with inflammatory trachoma (p=0.0410), while the G allele (p=0.0410) was associated with protection. Conclusion TLR4 and MICA may modulate the risk of severity to trachoma disease by modulating the immune response to Ct. In addition; the increased frequency of MICA-A9 heterozygote in controls may suggest a positive selection of these alleles in adaptation to environments where Ct is endemic. PMID:27559544

Conservation of human chromosome 13 polymorphic microsatellite (CA){sub n} repeats in chimpanzees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deka, R.; Shriver, M.D.; Yu, L.M.

Tandemly repeated (dC-dA){sub n} {center_dot} (dG-dT){sub n} sequences occur abundantly and are found in most eukaryotic genomes. To investigate the level of conservation of these repeat sequences in nonhuman primates, the authors have analyzed seven human chromosome 13 dinucleotide (CA){sub n} repeat loci in chimpanzees by DNA amplification using primers designed for analysis of human loci. Comparable levels of polymorphism at these loci in the two species, revealed by the number of alleles, heterozygosity, and allele sizes, suggest that the (CA){sub n} repeat arrays and their genomic locations are highly conserved. Even though the proportion of shared alleles between themore » two species varies enormously and the modal alleles are not the same, allelic lengths at each locus in the chimpanzees are detected within the bounds of the allele size range observed in humans. A similar observation has been noted in a limited number of gorillas and orangutans. Using a new measure of genetic distance that takes into account the size of alleles, they have compared the genetic distance between humans and chimpanzees. The genetic distance between these two species was found to be ninefold smaller than expected assuming there is no selection or mutational bias toward retention of (CA){sub n} repeat arrays. These findings suggest a functional significance for these microsatellite loci. 34 refs., 1 fig., 2 tabs.« less

Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut

USDA-ARS?s Scientific Manuscript database

One hundred and forty-seven primer pairs originally designed to amplify microsatellites, also known as simple sequence repeats (SSR), in black walnut (Juglans nigra L.) were screened for utility in persian walnut (J. regia L.). Based on scorability and number of informative polymorphisms, the best 1...

De novo genome assembly of Cercospora beticola for microsatellite marker development and validation

USDA-ARS?s Scientific Manuscript database

Cercospora leaf spot caused by Cercospora beticola is a significant threat to the production of sugar and table beet worldwide. A de novo genome assembly of C. beticola was used to develop eight polymorphic and reproducible microsatellite markers for population genetic analyses. These markers were u...

Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci.

PubMed

Dubé, Caroline E; Planes, Serge; Zhou, Yuxiang; Berteaux-Lecellier, Véronique; Boissin, Emilie

2017-01-01

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla , an important reef-builder of Indo-Pacific reefs . We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2-13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323-0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Characterization of 21 microsatellite markers from cogongrass, Imperata cylindrica (Poaceae), a weed species distributed worldwide.

PubMed

Chiang, Yu-Chung; Tsai, Chi-Chu; Hsu, Tsai-Wen; Chou, Chang-Hung

2012-11-01

Microsatellite loci were developed from Imperata cylindrica, a traditional medicinal herb in Asia and among the top 10 worst invasive weeds in the world, to aid in the identification of the limits of asexual clonal individuals. A total of 21 microsatellite markers, including 18 polymorphic and three monomorphic loci, were developed from I. cylindrica using a magnetic bead enrichment protocol. The primers amplified dinucleotide, trinucleotide, and complex repeats. The number of alleles ranged from one to 19 per locus, with an observed heterozygosity ranging from 0.09 to 1.00. Several loci deviated significantly from the within-population Hardy-Weinberg equilibrium as a result of asexual clonal reproduction. These polymorphic markers should be useful tools in further studies on the identification of the range of clonal reproduction units and the selection and classification of the medicinal cultivar.

Development and characterization of microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla

PubMed Central

Byers, James E.; Greig, Thomas W.; Strand, Allan E.; Weinberger, Florian

2015-01-01

Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid–diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid–diploid primary producer. PMID:26339541

Development and characterization of 16 polymorphic microsatellite markers from Taiwan cow-tail fir, Keteleeria davidiana var. formosana (Pinaceae) and cross-species amplification in other Keteleeria taxa

PubMed Central

2014-01-01

Background Keteleeria davidiana var. formosana (Pinaceae), Taiwan cow-tail fir, is an endangered species listed on the IUCN Red List of Threatened Species and only two populations remain, both on the Taiwan Island. Sixteen polymorphic microsatellite loci were developed in an endangered and endemic gymnosperm species, Keteleeria davidiana var. formosana, and were tested in an additional 6 taxa, K. davidiana var. calcarea, K. davidiana var. chienpeii, K. evelyniana, K. fortunei, K. fortunei var. cyclolepis, and K. pubescens, to evaluate the genetic variation available for conservation management and to reconstruct the phylogeographic patterns of this ancient lineage. Findings Polymorphic primer sets were developed from K. davidiana var. formosana using the modified AFLP and magnetic bead enrichment method. The number of alleles ranged from 3 to 16, with the observed heterozygosity ranging from 0.28 to 1.00. All of the loci were found to be interspecifically amplifiable. Conclusions These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct evolutionary units within species and establishing the phylogeographic patterns and the process of speciation among closely related species. PMID:24755442

Molecular mapping and breeding with microsatellite markers.

PubMed

Lightfoot, David A; Iqbal, Muhammad J

2013-01-01

In genetics databases for crop plant species across the world, there are thousands of mapped loci that underlie quantitative traits, oligogenic traits, and simple traits recognized by association mapping in populations. The number of loci will increase as new phenotypes are measured in more diverse genotypes and genetic maps based on saturating numbers of markers are developed. A period of locus reevaluation will decrease the number of important loci as those underlying mega-environmental effects are recognized. A second wave of reevaluation of loci will follow from developmental series analysis, especially for harvest traits like seed yield and composition. Breeding methods to properly use the accurate maps of QTL are being developed. New methods to map, fine map, and isolate the genes underlying the loci will be critical to future advances in crop biotechnology. Microsatellite markers are the most useful tool for breeders. They are codominant, abundant in all genomes, highly polymorphic so useful in many populations, and both economical and technically easy to use. The selective genotyping approaches, including genotype ranking (indexing) based on partial phenotype data combined with favorable allele data and bulked segregation event (segregant) analysis (BSA), will be increasingly important uses for microsatellites. Examples of the methods for developing and using microsatellites derived from genomic sequences are presented for monogenic, oligogenic, and polygenic traits. Examples of successful mapping, fine mapping, and gene isolation are given. When combined with high-throughput methods for genotyping and a genome sequence, the use of association mapping with microsatellite markers will provide critical advances in the analysis of crop traits.

Response to competition of bulbous geophyte Allium oleraceum differing in ploidy level.

PubMed

Fialová, M; Duchoslav, M

2014-01-01

Experimental studies that explore the possible causes of ploidy distributions and niche differentiation are rare. Increased competitive ability may be advantageous for survival in dense vegetation and may strongly affect local and regional abundances of cytotypes and potentially contribute to invasion success. We compared survival, growth and reproduction of plants originating from bulbils of three cytotypes (2n = 4x, 5x, 6x) of Allium oleraceum growing with and without a competitor (Arrhenatherum elatius). There was a strong negative effect of competition but no effect of ploidy or ploidy × competition on survivorship, height and total dry mass of A. oleraceum, i.e. no support for different competitive abilities of the ploidy levels. However, slightly different responses of populations to competition treatments within all cytotypes suggest differentiation within cytotypes. Under competition, plant survivorship was low, surviving plants were small, had low dry mass and produced neither sexual nor asexual propagules. Without competition, plant survivorship was high, and cytotypes differed in three traits after 2 year's growth: dry mass of flowers, number of flowers and ratio of the dry mass of sexual to asexual propagules all decreased with increasing ploidy level. We additionally tested tetra- and pentaploids as to whether plants originating from different types of propagule (bulbils, seeds) differ in survivorship, growth and reproduction when growing with and without a competitor. Plants originating from bulbils had higher survivorship, were more robust, flowered earlier and produced more propagules when compared to plants originating from seeds and grown without competition. Under competition, differences in performance between plants originating from seeds and bulbils mostly disappeared, with higher survivorship only for plants originating from bulbils. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

Isolation and characterization of 10 microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean relict plant.

PubMed

García-Fernández, Alfredo; Lázaro-Nogal, Ana; Traveset, Anna; Valladares, Fernando

2012-08-01

The main aim of this study was to isolate and characterize microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean shrub relict of the early Tertiary, which inhabits western Mediterranean islands and coasts. Microsatellites will be useful for investigating biogeography and landscape genetics across the species distribution range, including current or past gene flow. Seventeen microsatellite loci were characterized, of which 10 were polymorphic and amplified for a total of 56 alleles in three populations of C. tricoccon. The markers revealed average coefficients of expected heterozygosity (H(e) = 0.425), observed heterozygosity (H(o) = 0.282), and inbreeding coefficient value per population (F(IS) = 0.408). These microsatellite primers will potentially be useful in the study of population and landscape genetics, conservation status of isolated populations, island-continental distribution, current or historical movements between populations, and in the investigation of the consequences of dispersal mechanisms of these plants.

Development of Eighteen Microsatellite Markers in Anemone amurensis (Ranunculaceae) and Cross-Amplification in Congeneric Species

PubMed Central

Sun, Mingzhou; Yin, Xiao; Shi, Fengxue; Li, Lin; Li, Mingrui; Li, Linfeng; Xiao, Hongxing

2012-01-01

Polyploidy plays an important role in the evolution of plant genomes. To enable the investigation of the polyploidy events within the genus Anemone, we developed eighteen microsatellite markers from the hexaploid species A. amurensis (Ranunculaceae), and tested their transferability in five closely related species. The number of total alleles (NA) for each resulting locus varied from one to eight. The polymorphism information content (PIC) and Nei’s genetic diversity (NGD) for these microsatellites ranged from 0.00 to 0.71 and 0.00 to 0.91, respectively. For each population, the NA was one to seven, and the values of PIC and NGD varied from 0.00 to 0.84 and 0.00 to 0.95, respectively. In addition, most of these microsatellites can be amplified successfully in the congeneric species. These microsatellite primers provide us an opportunity to study the polyploid evolution in the genus Anemone. PMID:22606017

Development of eighteen microsatellite markers in Anemone amurensis (Ranunculaceae) and cross-amplification in congeneric species.

PubMed

Sun, Mingzhou; Yin, Xiao; Shi, Fengxue; Li, Lin; Li, Mingrui; Li, Linfeng; Xiao, Hongxing

2012-01-01

Polyploidy plays an important role in the evolution of plant genomes. To enable the investigation of the polyploidy events within the genus Anemone, we developed eighteen microsatellite markers from the hexaploid species A. amurensis (Ranunculaceae), and tested their transferability in five closely related species. The number of total alleles (N(A)) for each resulting locus varied from one to eight. The polymorphism information content (PIC) and Nei's genetic diversity (N(GD)) for these microsatellites ranged from 0.00 to 0.71 and 0.00 to 0.91, respectively. For each population, the N(A) was one to seven, and the values of PIC and N(GD) varied from 0.00 to 0.84 and 0.00 to 0.95, respectively. In addition, most of these microsatellites can be amplified successfully in the congeneric species. These microsatellite primers provide us an opportunity to study the polyploid evolution in the genus Anemone.

Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers

PubMed Central

Agung, Paskah Partogi; Saputra, Ferdy; Septian, Wike Andre; Lusiana; Zein, Moch. Syamsul Arifin; Sulandari, Sri; Anwar, Saiful; Wulandari, Ari Sulistyo; Said, Syahruddin; Tappa, Baharuddin

2016-01-01

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia. PMID:26732442

BAT-25 polymorphism in Chinese from Jiangsu province and its implication for locus microsatellite instability screening.

PubMed

Zheng, Yan Ying; Xie, Ling; Liu, Li; Zhang, Shu Peng; Wu, Xiao Bin; Zhu, Chang Le; Lai, Ren Sheng

2012-10-08

Colorectal cancer is one of the most common tumors with high mortality in China. Microsatellite instability (MSI) analysis is important for the diagnosis of hereditary non-polyposis colorectal cancer (HNPCC) and for the prediction of 5-FU chemotherapy efficiency of colorectal tumors, especially in terms of therapeutic response and overall survival rates. Among the MSI markers recommended by the NIH/NCI, BAT-25 has been extensively studied for its major role in MSI. BAT-25 presents different polymorphisms in different ethnic populations and studies of its polymorphisms in the Chinese population are still very limited. To analyze the frequency of constitutive polymorphic variation at the BAT-25 locus in Chinese from Jiangsu Province and its implication for locus MSI screening. The frequency of allelic variation at the BAT-25 locus of cervical cells from 500 healthy women and blood from 16 healthy males was assessed by direct sequencing. Twenty samples were also analyzed by fragment analysis. DNA extracted from blood of 94 patients with gastrointestinal cancer or endometrial cancer was analyzed by fragment analysis. After comparison with the sequencing results, the more frequent allele lengths were 126-127 bp, 128-129 bp, 129-130 bp, respectively consistent with the 24 poly(T) (T24), T25 and T26 alleles. At the BAT-25 locus, 516 healthy individuals had respectively 1.36%, 97.28% and 1.36% of the T24, T25 and T26. Whereas for the 94 cancer patients allelic frequencies were 0.53%, 1.06%, 96.8%, 1.6% for T15, T24, T25 and T26 alleles respectively. Sixteen healthy males had only the T25 allele and heterozygous T15 was only found in 1 male patient with colon cancer. We established the relation between fragment length and thymine repeats in BAT-25. The results showed that the BAT-25 locus is quasimonomorphic in Chinese from Jiangsu province. Moreover we showed that variant alleles of BAT-25 were found more likely in blood from cancer patients than in healthy individuals

Development of 12 genic microsatellite loci for a biofuel grass, Miscanthus sinensis (Poaceae).

PubMed

Ho, Chuan-Wen; Wu, Tai-Han; Hsu, Tsai-Wen; Huang, Jao-Ching; Huang, Chi-Chun; Chiang, Tzen-Yuh

2011-08-01

Miscanthus, a nonfood plant with high potential as a biofuel, has been used in Europe and the United States. The selection of a cultivar with high biomass, photosynthetic efficiency, and stress resistance from wild populations has become an important issue. New genic microsatellite markers will aid the assessment of genetic diversity for different strains. Twelve polymorphic microsatellite markers derived from the transcriptome of Miscanthus sinensis fo. glaber were identified and screened on 80 individuals of M. sinensis. The number of alleles per locus ranged from 6 to 12, and the mean expected heterozygosity was 0.75. Cross-taxa transferability revealed that all loci can be applied to all varieties of M. sinensis, as well as the closely related species M. floridulus. These new genic microsatellite markers are useful for characterizing different traits in breeding programs or to select genes useful for biofuel.

CHARACTERIZATION OF SEVEN POLYMORPHIC MICROSATELLITE LOCI IN THE COMMON LOON (GAVIA IMMER)

EPA Science Inventory

We describe polymerase chain reaction (PCR) primers and conditions to amplify seven microsatellite DNA loci isolated from the Common Loon (Gavia immer). The PCR primers were tested on 83 individuals from ten locations in North America, including breeding, migration stopover, and...

Haplogroup-specific deviation from the stepwise mutation model at the microsatellite loci DYS388 and DYS392.

PubMed

Nebel, A; Filon, D; Hohoff, C; Faerman, M; Brinkmann, B; Oppenheim, A

2001-01-01

Deviation from the stepwise mutation model (SMM) at specific human microsatellite loci has implications for population genetic and forensic investigations. In the present study, data on six Y chromosome-specific microsatellites were pooled for 455 paternally unrelated males from six Middle Eastern populations. All chromosomes were assigned to three haplogroups defined by six binary polymorphisms. Two of the microsatellite loci tested, DYS388 and DYS392, displayed marked haplogroup-specific differences in their allele variability. A bimodal distribution of short and long alleles was observed for DYS388 in haplogroup 1 and for DYS392 in haplogroups 1 and 2. Further investigation showed that the short/long alleles segregated almost completely between genealogically distinct haplogroups defined by additional binary markers. Thus, these two loci have a discriminatory power similar to a binary polymorphism. DYS388 was characterised by an extremely low mutation rate in haplogroups 2 and 3, as was DYS392 in haplogroup 3. Sequence analysis of the repeat regions at the two loci revealed no irregularities, indicating that the triplet expansion in these loci is not controlled by sequence variation at the repeat level. A high frequency of long DYS388 alleles has, so far, been found only in populations originating in the Middle East, suggesting that this microsatellite is useful as a region-specific marker.

Development of microsatellite markers for Anadenanthera colubrina (Leguminosae), a neotropical tree species.

PubMed

Feres, Juliana Massimino; Monteiro, Mariza; Zucchi, Maria I; Pinheiro, José B; Mestriner, Moacyr A; Alzate-Marin, Ana Lilia

2012-04-01

We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeirão Preto in São Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.

Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus) and current genetic status of this species in Vietnam.

PubMed

Nguyen, Trung Thanh; Genini, Sem; Bui, Linh Chi; Voegeli, Peter; Stranzinger, Gerald; Renard, Jean-Paul; Maillard, Jean-Charles; Nguyen, Bui Xuan

2007-11-06

The wild gaur (Bos gaurus) is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci. One hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90%) with a total of 264 alleles, and of these, 68 (58.1%) gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189) distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861) were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC) values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho) ranged from 0.091 to 0.909 (mean of 0.269). Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively. Extensive conservation of cattle microsatellite loci in the wild gaur

Cross-amplified microsatellites in the European cherry fly, Rhagoletis cerasi: medium polymorphic-highly informative markers.

PubMed

Augustinos, A A; Asimakopoulou, A K; Papadopoulos, N T; Bourtzis, K

2011-02-01

The European cherry fruit fly, Rhagoletis cerasi (Diptera: Tephritidae), is a major pest of cherries in Europe and parts of Asia. Despite its big economic significance, there is a lack of studies on the genetic structure of its natural populations. Knowledge about an insect pest on molecular, genetic and population levels facilitates the development of environmentally friendly control methods. In this study, we present the development of 13 microsatellite markers for R. cerasi, through cross-species amplification. These markers have been used for the genotyping of 130 individuals from five different sampling sites in Greece. Our results indicate that (i) cross-species amplification is a versatile and rapid tool for developing microsatellite markers in Rhagoletis spp., (ii) the microsatellite markers presented here constitute an important tool for population studies on this pest, and (iii) there is clear structuring of natural European cherry fly populations.

DNA polymorphisms at bermudagrass microsatellite loci and their use in genotype fingerprinting

USDA-ARS?s Scientific Manuscript database

The economically important, turf-type bermudagrasses include diploid Cynodon transvaalensis, tetraploid C. dactylon, and sterile triploid hybrids produced by crosses of these species. The objective of this study was to develop a set of microsatellite markers that could be used to distinguish among c...

Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study.

PubMed

Mishra, Sudhanshu; Singh, Sujeet Kumar; Munjal, Ashok Kumar; Aspi, Jouni; Goyal, Surendra Prakash

2014-01-03

In India, six landscapes and source populations that are important for long-term conservation of Bengal tigers (Panthera tigris tigris) have been identified. Except for a few studies, nothing is known regarding the genetic structure and extent of gene flow among most of the tiger populations across India as the majority of them are small, fragmented and isolated. Thus, individual-based relationships are required to understand the species ecology and biology for planning effective conservation and genetics-based individual identification has been widely used. But this needs screening and describing characteristics of microsatellite loci from DNA from good-quality sources so that the required number of loci can be selected and the genotyping error rate minimized. In the studies so far conducted on the Bengal tiger, a very small number of loci (n = 35) have been tested with high-quality source of DNA, and information on locus-specific characteristics is lacking. The use of such characteristics has been strongly recommended in the literature to minimize the error rate and by the International Society for Forensic Genetics (ISFG) for forensic purposes. Therefore, we describe for the first time locus-specific genetic and genotyping profile characteristics, crucial for population genetic studies, using high-quality source of DNA of the Bengal tiger. We screened 39 heterologous microsatellite loci (Sumatran tiger, domestic cat, Asiatic lion and snow leopard) in captive individuals (n = 8), of which 21 loci are being reported for the first time in the Bengal tiger, providing an additional choice for selection. The mean relatedness coefficient (R = -0.143) indicates that the selected tigers were unrelated. Thirty-four loci were polymorphic, with the number of alleles ranging from 2 to 7 per locus, and the remaining five loci were monomorphic. Based on the PIC values (> 0.500), and other characteristics, we suggest that 16 loci (3 to 7 alleles) be used for genetic

Successful development of microsatellite markers in a challenging species: the horizontal borer Austroplatypus incompertus (Coleoptera: Curculionidae).

PubMed

Smith, S; Joss, T; Stow, A

2011-10-01

The analysis of microsatellite loci has allowed significant advances in evolutionary biology and pest management. However, until very recently, the potential benefits have been compromised by the high costs of developing these neutral markers. High-throughput sequencing provides a solution to this problem. We describe the development of 13 microsatellite markers for the eusocial ambrosia beetle, Austroplatypus incompertus, a significant pest of forests in southeast Australia. The frequency of microsatellite repeats in the genome of A. incompertus was determined to be low, and previous attempts at microsatellite isolation using a traditional genomic library were problematic. Here, we utilised two protocols, microsatellite-enriched genomic library construction and high-throughput 454 sequencing and characterised 13 loci which were polymorphic among 32 individuals. Numbers of alleles per locus ranged from 2 to 17, and observed and expected heterozygosities from 0.344 to 0.767 and from 0.507 to 0.860, respectively. These microsatellites have the resolution required to analyse fine-scale colony and population genetic structure. Our work demonstrates the utility of next-generation 454 sequencing as a method for rapid and cost-effective acquisition of microsatellites where other techniques have failed, or for taxa where marker development has historically been both complicated and expensive.

Development and characterization of microsatellite markers for rice leaffolder, Cnaphalocrocis medinalis (Guenée) and cross-species amplification in other Pyralididae.

PubMed

An, Baoguang; Deng, Xiaolong; Shi, Huiyun; Ding, Meng; Lan, Jie; Yang, Jing; Li, Yangsheng

2014-02-01

Rice leaffolder, Cnaphalocrocis medinalis (Guenée), is a destructive and widespread pest on rice. In this study, 20 microsatellite markers were isolated and characterized from C. medinalis partial genomic libraries using the method of fast isolation by AFLP of sequence containing repeats. Of these markers, 18 markers displayed polymorphisms. Polymorphisms were evaluated in 48 individuals from two natural populations. The number of alleles per locus ranged from 2 to 15, and the expected and observed heterozygosities ranged from 0.324 to 0.934 and from 0.304 to 0.917, respectively. Cross-species amplification was also performed to test the transferability of the 20 microsatellite markers and a moderate level of cross amplication was observed across the three species of Pyralididae (26.67 %). These microsatellite loci would facilitate the future study on population genetics and molecular genetics of rice leaffolder and would also be useful for study in Chilo suppressalis, Scirpophaga incertulas and Pyrausta nubilalis.

Increasing genetic gain by reducing ploidy in potato

USDA-ARS?s Scientific Manuscript database

While potato cultivars in major world production regions are tetraploid, wild and cultivated potatoes in the crop’s center of origin range from diploid to hexaploid. Landrace potato varieties cannot be distinguished based on ploidy. Contrary to popular belief, tetraploidy does not appear to be neces...

SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of plant specialty crops.

PubMed

Kuhn, David N; Motamayor, Juan Carlos; Meerow, Alan W; Borrone, James W; Schnell, Raymond J

2008-10-01

For well-studied plant species with whole genome sequence or extensive EST data, SNP markers are the logical choice for both genotyping and whole genome association studies. However, SNP markers may not address the needs of researchers working on specialty crops with limited available genomic information. Microsatellite markers have been frequently employed due to their robustness, but marker development can be difficult and may result in few polymorphic markers. SSCP markers, such as microsatellites, are PCR-based and scored by electrophoretic mobility but, because they are based on SNPs rather than length differences, occur more frequently and are easier to develop than microsatellites. We have examined how well correlated the estimation of genetic diversity and genetic distance are in a population or germplasm collection when measured by 13 highly polymorphic microsatellite markers or 20 SSCP markers. We observed a significant correlation in pairwise genetic distances of 82 individuals in an international cacao germplasm collection (Mantel test Rxy=0.59, p<0.0001 for 10 000 permutations). Both sets of markers could distinguish each individual in the population. These data provide strong support for the use of SSCP markers in the genotyping of plant species where development of microsatellites would be difficult or expensive.

Application of novel polymorphic microsatellite loci identified in the Korean Pacific Abalone (Haliotis diversicolor supertexta (Haliotidae)) in the genetic characterization of wild and released populations.

PubMed

An, Hye Suck; Lee, Jang Wook; Hong, Seong Wan

2012-01-01

The small abalone, Haliotis diversicolor supertexta, of the family Haliotidae, is one of the most important species of marine shellfish in eastern Asia. Over the past few decades, this species has drastically declined in Korea. Thus, hatchery-bred seeds have been released into natural coastal areas to compensate for the reduced fishery resources. However, information on the genetic background of the small abalone is scarce. In this study, 20 polymorphic microsatellite DNA markers were identified using next-generation sequencing techniques and used to compare allelic variation between wild and released abalone populations in Korea. Using high-throughput genomic sequencing, a total of 1516 (2.26%; average length of 385 bp) reads containing simple sequence repeats were obtained from 86,011 raw reads. Among the 99 loci screened, 28 amplified successfully, and 20 were polymorphic. When comparing allelic variation between wild and released abalone populations, a total of 243 different alleles were observed, with 18.7 alleles per locus. High genetic diversity (mean heterozygosity = 0.81; mean allelic number = 15.5) was observed in both populations. A statistical analysis of the fixation index (F(ST)) and analysis of molecular variance (AMOVA) indicated limited genetic differences between the two populations (F(ST) = 0.002, p > 0.05). Although no significant reductions in the genetic diversity were found in the released population compared with the wild population (p > 0.05), the genetic diversity parameters revealed that the seeds released for stock abundance had a different genetic composition. These differences are likely a result of hatchery selection and inbreeding. Additionally, all the primer pair sets were effectively amplified in another congeneric species, H. diversicolor diversicolor, indicating that these primers are useful for both abalone species. These microsatellite loci may be valuable for future aquaculture and population genetic studies aimed at

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century1

PubMed Central

Hodel, Richard G. J.; Segovia-Salcedo, M. Claudia; Landis, Jacob B.; Crowl, Andrew A.; Sun, Miao; Liu, Xiaoxian; Gitzendanner, Matthew A.; Douglas, Norman A.; Germain-Aubrey, Charlotte C.; Chen, Shichao; Soltis, Douglas E.; Soltis, Pamela S.

2016-01-01

Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers. PMID:27347456

Genetic variability in Brazilian wheat cultivars assessed by microsatellite markers

PubMed Central

2009-01-01

Wheat (Triticum aestivum) is one of the most important food staples in the south of Brazil. Understanding genetic variability among the assortment of Brazilian wheat is important for breeding. The aim of this work was to molecularly characterize the thirty-six wheat cultivars recommended for various regions of Brazil, and to assess mutual genetic distances, through the use of microsatellite markers. Twenty three polymorphic microsatellite markers (PMM) delineated all 36 of the samples, revealing a total of 74 simple sequence repeat (SSR) alleles, i.e. an average of 3.2 alleles per locus. Polymorphic information content (PIC value) calculated to assess the informativeness of each marker ranged from 0.20 to 0.79, with a mean of 0.49. Genetic distances among the 36 cultivars ranged from 0.10 (between cultivars Ocepar 18 and BRS 207) to 0.88 (between cultivars CD 101 and Fudancep 46), the mean distance being 0.48. Twelve groups were obtained by using the unweighted pair-group method with arithmetic means analysis (UPGMA), and thirteen through the Tocher method. Both methods produced similar clusters, with one to thirteen cultivars per group. The results indicate that these tools may be used to protect intellectual property and for breeding and selection programs. PMID:21637519

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

USDA-ARS?s Scientific Manuscript database

Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective o...

Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L. osseus) of Lepisosteidae

USGS Publications Warehouse

Moyer, G.R.; Sloss, Brian L.; Kreiser, B.R.; Feldheim, K.A.

2009-01-01

We report on the isolation of 17 polymorphic microsatellite loci from alligator gar (Atractosteus spatula), a large-bodied species that has experienced population declines across much of its range. These loci possessed 2-19 alleles and observed heterozygosities of 0-0.974. All loci conformed to Hardy-Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Nine and eight of these loci were found to be polymorphic in the related species Lepisosteus oculatus and L. osseus, respectively. These microsatellite loci should prove useful in conservation efforts of A. spatula through the study of population structure and hatchery broodstock management. ?? 2009 Blackwell Publishing Ltd.

Isolation of microsatellite loci for Rhodiola alsia (Crassulaceae), an important ethno-medicinal herb endemic to the Qinghai-Tibetan plateau.

PubMed

Zhang, F Q; Lei, S Y; Gao, Q B; Khan, G; Xing, R; Yang, H L; Chen, S L

2015-05-18

Rhodiola alsia, which has been used widely in traditional Chinese medicine for a considerable time, grows on moist habitats at high altitude near the snow line. Microsatellite loci were developed for R. alsia to investigate its population genetics. In total, 17 polymorphic microsatellites were developed based on ESTs from the Illumina HiSeq(TM) 2000 platform. The microsatellite loci were checked for variability using 80 individuals of R. alsia sampled from four locations on the Qinghai-Tibet Plateau. The total number of alleles per locus ranged from 10 to 20, and the observed heterozygosity ranged from 0.000 to 1.000. The null allele frequency ranged from 0.000 to 0.324. These microsatellites are expected to be helpful in future studies of population genetics in R. alsia and related species.

[Genetic diversity of DNA microsatellite for Tibetan Yak].

PubMed

Li, Duo; Chai, Zhi-Xin; Ji, Qiu-Mei; Zhang, Cheng-Fu; Xin, Jin-Wei; Zhong, Jin-Cheng

2013-02-01

To assess the genetic diversity and relationship of the Tibetan yak breeds. The genetic diversity and phylogenies of a total of 480 individual from 11 Tibetan yak groups were analyzed using PCR and multiplex gel electrophoresis of silver staining technology with eight pairs of microsatellite markers.The result showed that these markers were highly polymorphic loci with rich genetic diversity in the Tibetan yak populations.The average polymorphic information content (PIC) in 11 groups of yak were higher than 0.5. The highest HEL13 was 0.8496, and the lowest TGLA57 was 0.7349. Among them, the PICof Dingqing yak was minimum (0.7505), indicating that the group is relatively pure.Sangri Yak had the highest PIC value (0.7949) indicating greater genetic variationwithinthe groups. Among the 11 groups examined, the order of heterozygosity size wasSangri(0.8193)>Jiangda(0.8190)>Sangsang(0.8157)>Baqing(0.8150)>Kangbu(0.8123)> Jiali(0.8087)>Gongbujiangda(0.8054)>Sibu(0.8041)>Leiwuqi(0.8033)>Pali(0.8031)>Dingqing(0.7831). The groups from eastern Tibet had grater genetic diversity than those from Western Tibet, which indicate that Tibet may be one of the cradles of the yak.According to the genetic distance, the cluster relationship constructed with UPGMA and NJ methods showed that 11 yak groups in Tibet could be divided into three forms. In summary,Tibet yak has abundant genetic diversity and the selected microsatellite markers can be used to evaluategenetic diversity of Tibetan yak.

PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis).

PubMed

Ramey, A; Graziano, S L; Nielsen, J L

2008-03-01

Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco. © 2007 Blackwell Publishing Ltd No claim to original US government works.

Host ploidy, parasitism and immune defence in a coevolutionary snail-trematode system.

PubMed

Osnas, E E; Lively, C M

2006-01-01

We studied the role of host ploidy and parasite exposure on immune defence allocation in a snail-trematode system (Potamopyrgus antipodarum-Microphallus sp.). In the field, haemocyte (the defence cell) concentration was lowest in deep-water habitats where infection is relatively low and highest in shallow-water habitats where infection is common. Because the frequency of asexual triploid snails is positively correlated with depth, we also experimentally studied the role of ploidy by exposing both diploid sexual and triploid asexual snails to Microphallus eggs. We found that triploid snails had lower haemocyte concentrations than did diploids in both parasite-addition and parasite-free treatments. We also found that both triploids and diploids increased their numbers of large granular haemocytes at similar rates after parasite exposure. Because triploid P. antipodarum have been shown to be more resistant to allopatric parasites than diploids, the current results suggest that the increased resistance of triploids is because of intrinsic genetic properties rather than to greater allocation to defence cells. This finding is consistent with recent theory on the advantages of increased ploidy for hosts combating coevolving parasites.

Isolation and characterization of new microsatellite markers in red tail prawn, Fenneropenaeus penicillatus, an endangered species in China.

PubMed

Yuan, Y; Shangguan, J B; Li, Z B; Ning, Y F; Huang, Y S; Li, B B; Mao, X Q

2015-11-30

Until recently, Fenneropenaeus penicillatus was considered a commercial shrimp species. However, in 2005, it was included on the Red List as an endangered species by the Chinese government. In this study, 19 new microsatellite markers in F. penicillatus were developed and tested in samples of 32 wild individuals from Nanao, China. Twelve loci were polymorphic and 7 were monomorphic. Of the 12 polymorphic loci, the number of alleles per locus ranged from 3 to 6, with an average of 4.42 alleles per locus. The polymorphism information content ranged from 0.302 to 0.670, with a mean of 0.4817. The observed and expected heterozygosities ranged from 0.2250 to 0.8889 and from 0.1111 to 0.7750, respectively. Significant deviations from Hardy-Weinberg equilibrium (HWE, adjusted P < 0.0042) after a Bonferroni correction were observed in 3 loci (NA-9, NA-57, and NA-64), whereas the other 9 loci were in HWE. These new microsatellite markers will be useful in further research on the population genetic structure of F. penicillatus.

Characterization of microsatellite loci in Festuca gautieri (Poaceae) and transferability to F. eskia and F. xpicoeuropeana.

PubMed

Segarra-Moragues, José Gabriel; Catalán, Pilar

2011-12-01

Enriched genomic libraries were used to isolate and characterize microsatellite loci in Festuca gautieri, an important plant component of subalpine calcareous grasslands of the eastern Iberian Peninsula, the Pyrenees, and the Cantabrian Mountains. Microsatellites were required to investigate landscape genetics across its distribution range and at a narrower geographical scale within the Ordesa y Monte Perdido, Aigüestortes, and Picos de Europa Spanish national parks. Ten polymorphic microsatellite loci were characterized. They amplified a total of 116 alleles in a sample of 30 individuals of F. gautieri, showing high levels of genetic diversity (expected heterozygosity = 0.821). Cross-species transferability to two other close congeners, F. eskia and F ×picoeuropeana, increased the total number of alleles to 137. These taxa showed lower numbers of alleles but similar levels of genetic diversity to F. gautieri. These microsatellite primers will be useful in population and landscape genetics and in establishing conservation strategies for these characteristic elements of subalpine pastures.

Development and characterization of microsatellite markers for Hibiscus glaber Matsum. ex Nakai, an endemic tree species of the oceanic Bonin Islands, Japan.

PubMed

Ohtani, Masato; Tani, Naoki; Yoshimaru, Hiroshi

2008-11-01

Polymorphic microsatellite markers were developed for Hibiscus glaber, an endemic tree of the Bonin Islands. Eighty-seven of the 208 sequences from an enriched library were unique and containing microsatellites. Ten loci were proved to be highly polymorphic among 78 individuals from the Nishi-jima Island. Total exclusionary powers for the first and the second parents were 99.989% and 99.999%, respectively. Nine loci also amplified single fragment from genomic DNA of H. tiliaceus, a related and widespread congener. Our markers can be reliably used for the estimation of current gene flow within/among populations of the two woody Hibiscus species. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Characterization of microsatellite loci from two-spotted octopus Octopus bimaculatus Verrill 1883 from pyrosequencing reads

USGS Publications Warehouse

Domínguez-Contreras, J. F.; Munguía-Vega, A.; Ceballos-Vázquez, B. P.; Arellano-Martínez, M.; Culver, Melanie

2014-01-01

We characterized 22 novel microsatellite loci in the two-spotted octopus Octopus bimaculatus using 454 pyrosequencing reads. All loci were polymorphic and will be used in studies of marine connectivity aimed at increasing sustainability of the resource. The mean number alleles per locus was 13.09 (range 7–19) and observed heterozygosities ranged from 0.50 to 1.00. Four loci pairs were linked and three deviated from Hardy–Weinberg equilibrium. Eighteen and 12 loci were polymorphic in Octopus bimaculoides and Octopus hubbsorum, respectively.

Development of microsatellite markers in Cordia bifurcata (Boraginaceae) and cross-species amplification in Cordia inermis and Cordia pringlei.

PubMed

Spoon, Tracey R; Kesseli, Rick V

2008-09-01

We developed 16 microsatellite markers in Cordia bifurcata, a Central and South American shrub. The markers show low polymorphism in C. bifurcata, a species suspected of self-fertilization or apomixis. Of four polymorphic loci, three had only two alleles. However, current research indicates that these markers hold value for interpopulational comparisons of C. bifurcata and for analyses of congeners. In Cordia inermis, a dioecious or subdioecious shrub, seven of the markers produced interpretable amplification products of which five showed polymorphism. In Cordia pringlei, a distylous shrub, nine of the markers produced interpretable amplification products of which six showed polymorphism. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Development of microsatellite markers using next-generation sequencing for the columnar cactus Echinopsis chiloensis (Cactaceae).

PubMed

Ossa, Carmen G; Larridon, Isabel; Peralta, Gioconda; Asselman, Pieter; Pérez, Fernanda

2016-12-01

The aim of this study was to develop microsatellite markers as a tool to study population structure, genetic diversity and effective population size of Echinopsis chiloensis, an endemic cactus from arid and semiarid regions of Central Chile. We developed 12 polymorphic microsatellite markers for E. chiloensis using next-generation sequencing and tested them in 60 individuals from six sites, covering all the latitudinal range of this species. The number of alleles per locus ranged from 3 to 8, while the observed (Ho) and expected (He) heterozygosity ranged from 0.0 to 0.80 and from 0.10 to 0.76, respectively. We also detected significant differences between sites, with F ST values ranging from 0.05 to 0.29. Microsatellite markers will enable us to estimate genetic diversity and population structure of E. chiloensis in future ecological and phylogeographic studies.

Effects of ploidy level and haplotype on variation of photosynthetic traits: Novel evidence from two Fragaria species

PubMed Central

Gao, Song; Yan, Qiaodi; Chen, Luxi; Song, Yaobin; Fu, Chengxin; Dong, Ming

2017-01-01

To reveal the effects of ploidy level and haplotype on photosynthetic traits, we chose 175 genotypes of wild strawberries belonging to two haplotypes at two types of ploidy levels (diploidy and tetraploidy) and measured photosynthetic traits. Our results revealed that ploidy significantly affected the characteristics of light-response curves, CO2-response curves, and leaf gas exchange parameters, except intercellular CO2 concentration (Ci). Tetraploid species had a lower light saturation point (LSP) and CO2 saturation point (CSP), higher light compensation point (LCP), dark respiration (Rd), and CO2 compensation point (CCP) than diploid species. Furthermore, tetraploid species have lower photosynthetic capacity than diploid species, including net photosynthetic rate (Pn), stomatal conductivity (Gs), and transpiration rate (Tr). In addition, haplotype had a significant effect on LSP, CSP, Tr, and Ci as well as a significant interactive effect between ploidy and haplotype on the maximal photosynethic rate of the light-response curve and Rd. Most of the variance existed within haplotypes among individuals. These results suggest that polyploidization was the main driver for the evolution of photosynthesis with increasing ploidy level (i.e. from diploidy to tetraploidy in Fragaria species), while the origin of a chromosome could also affect the photosynthetic traits and the polyploidization effect on photosynthetic traits. PMID:28644876

Effects of ploidy level and haplotype on variation of photosynthetic traits: Novel evidence from two Fragaria species.

PubMed

Gao, Song; Yan, Qiaodi; Chen, Luxi; Song, Yaobin; Li, Junmin; Fu, Chengxin; Dong, Ming

2017-01-01

To reveal the effects of ploidy level and haplotype on photosynthetic traits, we chose 175 genotypes of wild strawberries belonging to two haplotypes at two types of ploidy levels (diploidy and tetraploidy) and measured photosynthetic traits. Our results revealed that ploidy significantly affected the characteristics of light-response curves, CO2-response curves, and leaf gas exchange parameters, except intercellular CO2 concentration (Ci). Tetraploid species had a lower light saturation point (LSP) and CO2 saturation point (CSP), higher light compensation point (LCP), dark respiration (Rd), and CO2 compensation point (CCP) than diploid species. Furthermore, tetraploid species have lower photosynthetic capacity than diploid species, including net photosynthetic rate (Pn), stomatal conductivity (Gs), and transpiration rate (Tr). In addition, haplotype had a significant effect on LSP, CSP, Tr, and Ci as well as a significant interactive effect between ploidy and haplotype on the maximal photosynethic rate of the light-response curve and Rd. Most of the variance existed within haplotypes among individuals. These results suggest that polyploidization was the main driver for the evolution of photosynthesis with increasing ploidy level (i.e. from diploidy to tetraploidy in Fragaria species), while the origin of a chromosome could also affect the photosynthetic traits and the polyploidization effect on photosynthetic traits.

Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus) and current genetic status of this species in Vietnam

PubMed Central

Nguyen, Trung Thanh; Genini, Sem; Bui, Linh Chi; Voegeli, Peter; Stranzinger, Gerald; Renard, Jean-Paul; Maillard, Jean-Charles; Nguyen, Bui Xuan

2007-01-01

Background The wild gaur (Bos gaurus) is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci. Results One hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90%) with a total of 264 alleles, and of these, 68 (58.1%) gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189) distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861) were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC) values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho) ranged from 0.091 to 0.909 (mean of 0.269). Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively. Conclusion Extensive conservation of cattle

A change of ploidy can modify epigenetic silencing.

PubMed Central

Mittelsten Scheid, O; Jakovleva, L; Afsar, K; Maluszynska, J; Paszkowski, J

1996-01-01

A silent transgene in Arabidopsis thaliana was reactivated in an outcross but not upon selfing of hemizygous plants. This result could only be explained by assuming a genetic difference between the transgene-free gametes of the wild-type and hemizygous transgenic plants, respectively, and led to the discovery of ploidy differences between the parental plants. To investigate whether a change of ploidy by itself can indeed influence gene expression, we performed crosses of diploid or tetraploid plants with a strain containing a single copy of a transgenic resistance gene in an active state. We observed reduced gene expression of the transgene in triploid compared with diploid hybrids. This led to loss of the resistant phenotype at various stages of seedling development in part of the population. The gene inactivation was reversible. Thus, an increased number of chromosomes can result in a new type of epigenetic gene inactivation, creating differences in gene expression patterns. We discuss the possible impact of this finding for genetic diploidization in the light of widespread, naturally occurring polyploidy and polysomaty in plants. Images Fig. 1 Fig. 2 PMID:8692954

Isolation of 18 microsatellite loci in the desert mistletoe Phoradendron californicum (Santalaceae) via 454 pyrosequencing1

PubMed Central

Arroyo, Juan M.; Munguia-Vega, Adrian; Rodríguez-Estrella, Ricardo; Bascompte, Jordi

2013-01-01

• Premise of the study: Microsatellite primers were developed for the parasitic mistletoe Phoradendron californicum to investigate to what extent population genetic structure depends on host tree distribution within a highly fragmented landscape. • Methods and Results: Fourteen unlinked polymorphic and four monomorphic nuclear microsatellite markers were developed using a genomic shotgun pyrosequencing method. A total of 187 alleles plus four monomorphic loci alleles were found in 98 individuals sampled in three populations from the Sonoran Desert in the Baja California peninsula (Mexico). Loci averaged 13.3 alleles per locus (range 4–28), and observed and expected heterozygosities within populations varied from 0.167–0.879 and 0.364–0.932, respectively. • Conclusions: Levels of polymorphism of the reported markers are adequate for studies of diversity and fragmentation in natural populations of this parasitic plant. Cross-species amplifications in P. juniperinum and P. diguetianum only showed four markers that could be useful in P. diguetianum. PMID:25202503

Development and characterization of microsatellite markers in the African forest elephant (Loxodonta cyclotis).

PubMed

Gugala, Natalie A; Ishida, Yasuko; Georgiadis, Nicholas J; Roca, Alfred L

2016-07-26

African elephants comprise two species, the savanna elephant (Loxodonta africana) and the forest elephant (L. cyclotis), which are distinct morphologically and genetically. Forest elephants are seriously threatened by poaching for meat and ivory, and by habitat destruction. However, microsatellite markers have thus far been developed only in African savanna elephants and Asian elephants, Elephas maximus. The application of microsatellite markers across deeply divergent lineages may produce irregular patterns such as large indels or null alleles. Thus we developed novel microsatellite markers using DNA from two African forest elephants. One hundred microsatellite loci were identified in next generation shotgun sequences from two African forest elephants, of which 53 were considered suitable for testing. Twenty-three microsatellite markers successfully amplified elephant DNA without amplifying human DNA; these were further characterized in 15 individuals from Lope National Park, Gabon. Three of the markers were monomorphic and four of them carried only two alleles. The remaining sixteen polymorphic loci carried from 3 to 8 alleles, with observed heterozygosity ranging from 0.27 to 0.87, expected heterozygosity from 0.40 to 0.86, and the Shannon diversity index from 0.73 to 1.86. Linkage disequilibrium was not detected between loci, and no locus deviated from Hardy-Weinberg equilibrium. The markers developed in this study will be useful for genetic analyses of the African forest elephant and contribute to their conservation and management.

The effects of warm temperature acclimation on constitutive stress, immunity, and metabolism in white sturgeon (Acipenser transmontanus) of different ploidies.

PubMed

Leal, Michaiah J; Clark, Brigitte E; Van Eenennaam, Joel; Schreier, Andrea D; Todgham, Anne E

2018-06-01

Previous studies suggest fish with additional copies of their genome (polyploids) underperform in suboptimal conditions and may be more susceptible to stress and disease. The objective of this study was to determine the role ploidy plays in the physiological response of white sturgeon to chronically elevated water temperatures. White sturgeon of two ploidies (8 N and 10 N) were acclimated to ambient (18 °C) and warm (22 °C) water. Bioindices of stress (plasma cortisol, glucose and lactate, total erythrocyte count, hematocrit, hemoglobin, mean erythrocyte volume, mean erythrocyte hemoglobin, and mean erythrocyte hemoglobin concentration), immunity (respiratory burst, plasma lysozyme, and total leukocyte count), and cellular metabolic capacity (lactate dehydrogenase and citrate synthase activity) were measured before and after a 6-week acclimation period. Both ploidies appear comparable in their constitutive immune and stress parameters and respond similarly to warming. Hematological indices suggest 8 N and 10 N sturgeon are similar in oxygen carrying capacity; however, differences in enzyme activity between ploidies indicate that 10 N sturgeon may have a lower cellular aerobic capacity. Our results have implications for the screening and management of ploidy on white sturgeon farms and hatcheries, as the differences between ploidies may affect 10 N sturgeon performance at elevated water temperatures. Further research is needed to elucidate the differences in inducible stress and immune responses and metabolism of white sturgeon of different ploidies. Copyright © 2018. Published by Elsevier Inc.

Thirteen nuclear microsatellite loci for butternut (Juglans cinerea L.).

PubMed

Hoban, Sean; Anderson, Robert; McCleary, Tim; Schlarbaum, Scott; Romero-Severson, Jeanne

2008-05-01

Butternut (Juglans cinerea L.) is an eastern North American forest tree severely threatened by an exotic fungal pathogen, Sirococcus clavigignenti-juglandacearum. We report here 13 nuclear microsatellites for genetic evaluation of the remaining natural populations. Summary statistics are reported for individuals from a population of butternuts in central Kentucky (N = 63). All markers were polymorphic, with an average of 13.7 alleles per locus observed. Four loci exhibited significantly fewer heterozygotes than expected under Hardy-Weinberg equilibrium (P < 0.05). © 2007 The Authors.

Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)

PubMed Central

Cuc, Luu M; Mace, Emma S; Crouch, Jonathan H; Quang, Vu D; Long, Tran D; Varshney, Rajeev K

2008-01-01

Background Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. Results A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. Conclusion Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be

Rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish, the mottled skate, Raja pulchra.

PubMed

Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

2012-01-01

The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1-10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni's correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.

Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra

PubMed Central

Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

2012-01-01

The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species. PMID:22837688

Fifty-three polymorphic microsatellite loci in the chestnut blight fungus, Cryphonectria parasitica

Treesearch

T.L. Kubisiak; C. Dutech; M.G. Milgroom

2006-01-01

We report on 53 microsatellite loci for use in population genetic or linkage mapping studies in Cryphonectria parasitica . In 40 isolates collected from throughout the Northern Hemisphere, the number of alleles per locus ranged from two to 14 (mean 5.17) with gene diversity values ranging from 0.049 to 0.859 (mean 0.437). Samples from Asia were more...

Characterization of microsatellite markers for the Restinga Antwren, Formicivora littoralis (Thamnophilidae), an endangered bird endemic to Brazil.

PubMed

Chaves, F G; Vecchi, M B; Webster, M S; Alves, M A S

2015-07-17

Molecular markers are important tools in determining parentage, gene flow, and the genetic structure of species. In the case of rare, endemic, and/or threatened species, these markers can be used to understand key ecological questions and support conservation actions. We developed seven microsatellite markers for the only bird endemic to the Restinga ecosystem. Microsatellite loci were isolated from a library that was based on 10 individuals (six males and four females). Primers were tested in 107 individuals of the same population. The number of alleles per locus ranged from 4 to 19, and the observed and expected heterozygosity varied from 0.15 to 0.84 and from 0.60 to 0.89, respectively. We expect that the polymorphic microsatellite loci we describe will be useful for other studies, particularly in the Tropics.

Isolation and characterization of microsatellite markers from the olive fly, Bactrocera oleae, and their cross-species amplification in the Tephritidae family

PubMed Central

Augustinos, Antonios A; Stratikopoulos, Elias E; Drosopoulou, Eleni; Kakani, Evdoxia G; Mavragani-Tsipidou, Penelope; Zacharopoulou, Antigone; Mathiopoulos, Kostas D

2008-01-01

Background The Tephritidae family of insects includes the most important agricultural pests of fruits and vegetables, belonging mainly to four genera (Bactrocera, Ceratitis, Anastrepha and Rhagoletis). The olive fruit fly, Bactrocera oleae, is the major pest of the olive fruit. Currently, its control is based on chemical insecticides. Environmentally friendlier methods have been attempted in the past (Sterile Insect Technique), albeit with limited success. This was mainly attributed to the lack of knowledge on the insect's behaviour, ecology and genetic structure of natural populations. The development of molecular markers could facilitate the access in the genome and contribute to the solution of the aforementioned problems. We chose to focus on microsatellite markers due to their abundance in the genome, high degree of polymorphism and easiness of isolation. Results Fifty-eight microsatellite-containing clones were isolated from the olive fly, Bactrocera oleae, bearing a total of sixty-two discrete microsatellite motifs. Forty-two primer pairs were designed on the unique sequences flanking the microsatellite motif and thirty-one of them amplified a PCR product of the expected size. The level of polymorphism was evaluated against wild and laboratory flies and the majority of the markers (93.5%) proved highly polymorphic. Thirteen of them presented a unique position on the olive fly polytene chromosomes by in situ hybridization, which can serve as anchors to correlate future genetic and cytological maps of the species, as well as entry points to the genome. Cross-species amplification of these markers to eleven Tephritidae species and sequencing of thirty-one of the amplified products revealed a varying degree of conservation that declines outside the Bactrocera genus. Conclusion Microsatellite markers are very powerful tools for genetic and population analyses, particularly in species deprived of any other means of genetic analysis. The presented set of

A novel and easy FxCycle™ violet based flow cytometric method for simultaneous assessment of DNA ploidy and six-color immunophenotyping.

PubMed

Tembhare, Prashant; Badrinath, Yajamanam; Ghogale, Sitaram; Patkar, Nikhil; Dhole, Nilesh; Dalavi, Pooja; Kunder, Nikesh; Kumar, Ashok; Gujral, Sumeet; Subramanian, P G

2016-03-01

Abnormal DNA ploidy is a valuable prognostic factor in many neoplasms, especially in hematological neoplasms like B-cell acute lymphoblastic leukemia (B-ALL) and multiple myeloma (MM). Current methods of flow-cytometric (FC) DNA-ploidy evaluation are either technically difficult or limited to three- to four-color immunophenotyping and hence, challenging to evaluate DNA-ploidy in minute tumor population with background rich of its normal counterpart cells and other hematopoietic cells. We standardized a novel sensitive and easy method of simultaneous evaluation of six- to seven-color immunophenotyping and DNA-ploidy using a dye-FxCycle Violet (FCV). Linearity, resolution, and coefficient of variation (CV) for FCV were studied using chicken erythrocyte nuclei. Ploidy results of FCV were compared with Propidium iodide (PI) in 20 samples and intra-assay variation for FCV was studied. Using this six-color immunophenotyping & FCV-protocol DNA-ploidy was determined in bone-marrow samples from 124 B-ALL & 50 MM patients. Dilution experiment was also conducted to determine the sensitivity in detection of aneuploidy in minute tumor population. FCV revealed high linearity and resolution in 450/50 channel. On comparison with PI, CV of Go/G1-peak with FCV (mean-CV 4.1%) was slightly higher than PI (mean-CV 2.9%) but had complete agreement in ploidy results. Dilution experiment showed that aneuploidy could be accurately detected up to the limit of 0.01% tumor cells. Intra-assay variation was very low with CV of 0.005%. In B-ALL, hypodiploidy was noted in 4%, hyperdiploidy in 24%, near-hyperdiploidy in 13% and remaining 59% were diploid. In MM, hypodiploidy was in 2%, hyperdiploidy in 58%, near-hyperdiploidy in 8% and remaining 30% were diploid. FCV-based DNA-ploidy method is a sensitive and easy method for simultaneous evaluation of six-color immunophenotyping and DNA analysis. It is useful in DNA-ploidy evaluation of minute tumor population in cases like minimal residual

Microsatellites for Carpotroche brasiliensis (Flacourtiaceae), a useful species for agroforestry and ecosystem conservation.

PubMed

Bittencourt, Flora; Alves, Jackeline S; Gaiotto, Fernanda A

2015-12-01

We developed microsatellite markers for Carpotroche brasiliensis (Flacourtiaceae), a dioecious tree that is used as a food resource by midsize animals of the Brazilian fauna. We designed 30 primer pairs using next-generation sequencing and classified 25 pairs as polymorphic. Observed heterozygosity ranged from 0.5 to 1.0, and expected heterozygosity ranged from 0.418 to 0.907. The combined probability of exclusion was greater than 0.999 and the combined probability of identity was less than 0.001, indicating that these microsatellites are appropriate for investigations of genetic structure, individual identification, and paternity testing. The developed molecular tools may contribute to future studies of population genetics, answering ecological and evolutionary questions regarding efficient conservation strategies for C. brasiliensis.

Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers.

PubMed

Palmieri, Darío A; Bechara, Marcelo D; Curi, Rogério A; Monteiro, Jomar P; Valente, Sérgio E S; Gimenes, Marcos A; Lopes, Catalina R

2010-01-01

Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

PubMed Central

2010-01-01

Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections. PMID:21637613

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

USDA-ARS?s Scientific Manuscript database

Microsatellite markers (MS) have traditionally been used for parental verification and are still the international standard in spite of their higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP) -based assays. Despite domestic and international demands fr...

MSH6 G39E Polymorphism and CpG Island Methylator Phenotype in Colon Cancer

PubMed Central

Curtin, Karen; Samowitz, Wade S.; Wolff, Roger K.; Caan, Bette J.; Ulrich, Cornelia M.; Potter, John D.; Slattery, Martha L.

2010-01-01

The MSH6 G39E germline polymorphism is not associated with an increased risk of either microsatellite stable or unstable sporadic colorectal cancer. Other than microsatellite instability, however, most genetic and epigenetic changes of tumors associated with this common variant have not been studied. The objective of our investigation was to evaluate associations between the MSH6 G39E (116G>A) polymorphism and CpG island methylator phenotype (CIMP) and BRAF V600E mutations in tumors from a sample of 1048 individuals with colon cancer and 1964 controls from Utah, Northern California, and Minnesota. The G39E polymorphism (rs1042821) was determined by the five prime nuclease assay. CIMP was determined by methylation-specific polymerase chain reaction (PCR) of CpG islands in MLH1, methylated in tumors (MINT)1, MINT2, MINT31, and CDKN2A. The BRAF V600E mutation was determined by sequencing exon 15. In microsatellite stable tumors, homozygous carriers of the G39E polymorphism had an increased risk of CIMP+ colon cancer (odds ratio (OR) 2.2, 95% confidence interval (CI) 1.1, 4.2) and BRAF V600E mutation (OR 3.1, 95% CI 1.01, 9.7) in a case–control comparison. This finding was not observed in unstable tumors; however, power may have been low to detect an association. Age at diagnosis, family history, and alcohol use did not interact with MSH6 G39E and CIMP. The MSH6 G39E germline polymorphism may be associated with CIMP+ colon cancer. PMID:19582761

Development of compound microsatellite markers in red-tide-causing dinoflagellate Akashiwo sanguinea (Dinophyceae).

PubMed

Cho, S-Y; Nagai, S; Nishitani, G; Han, M-S

2009-05-01

We isolated 13 polymorphic microsatellites from the red-tide causing dinoflagellate Akashiwo sanguinea. These loci were highly variable, with between 2 and 10 alleles per locus, and estimated gene diversity ranging from 0.08 to 0.82. These loci have the potential to reveal genetic structure and estimate gene flow among A. sanguinea populations. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Correlation between DNA ploidy, metaphase high-resolution comparative genomic hybridization results and clinical outcome of synovial sarcoma

PubMed Central

2011-01-01

Background Although synovial sarcoma is the 3rd most commonly occurring mesenchymal tumor in young adults, usually with a highly aggressive clinical course; remarkable differences can be seen regarding the clinical outcome. According to comparative genomic hybridization (CGH) data published in the literature, the simple and complex karyotypes show a correlation between the prognosis and clinical outcome. In addition, the connection between DNA ploidy and clinical course is controversial. The aim of this study was using a fine-tuning interpretation of our DNA ploidy results and to compare these with metaphase high-resolution CGH (HR-CGH) results. Methods DNA ploidy was determined on Feulgen-stained smears in 56 synovial sarcoma cases by image cytometry; follow up was available in 46 cases (average: 78 months). In 9 cases HR-CGH analysis was also available. Results 10 cases were found DNA-aneuploid, 46 were DNA-diploid by image cytometry. With fine-tuning of the diploid cases according to the 5c exceeding events (single cell aneuploidy), 33 cases were so called "simple-diploid" (without 5c exceeding events) and 13 cases were "complex-diploid"; containing 5c exceeding events (any number). Aneuploid tumors contained large numbers of genetic alterations with the sum gain of at least 2 chromosomes (A-, B- or C-group) detected by HR-CGH. In the "simple-diploid" cases no or few genetic alterations could be detected, whereas the "complex-diploid" samples numerous aberrations (equal or more than 3) could be found. Conclusions Our results show a correlation between the DNA-ploidy, a fine-tuned DNA-ploidy and the HR-CGH results. Furthermore, we found significant correlation between the different ploidy groups and the clinical outcome (p < 0.05). PMID:22053830

Polyploidy in the Olive Complex (Olea europaea): Evidence from Flow Cytometry and Nuclear Microsatellite Analyses

PubMed Central

Besnard, G.; Garcia-Verdugo, C.; Rubio De Casas, R.; Treier, U. A.; Galland, N.; Vargas, P.

2008-01-01

Background Phylogenetic and phylogeographic investigations have been previously performed to study the evolution of the olive tree complex (Olea europaea). A particularly high genomic diversity has been found in north-west Africa. However, to date no exhaustive study has been addressed to infer putative polyploidization events and their evolutionary significance in the diversification of the olive tree and its relatives. Methods Representatives of the six olive subspecies were investigated using (a) flow cytometry to estimate genome content, and (b) six highly variable nuclear microsatellites to assess the presence of multiple alleles at co-dominant loci. In addition, nine individuals from a controlled cross between two individuals of O. europaea subsp. maroccana were characterized with microsatellites to check for chromosome inheritance. Key Results Based on flow cytometry and genetic analyses, strong evidence for polyploidy was obtained in subspp. cerasiformis (tetraploid) and maroccana (hexaploid), whereas the other subspecies appeared to be diploids. Agreement between flow cytometry and genetic analyses gives an alternative approach to chromosome counting to determine ploidy level of trees. Lastly, abnormalities in chromosomes inheritance leading to aneuploid formation were revealed using microsatellite analyses in the offspring from the controlled cross in subsp. maroccana. Conclusions This study constitutes the first report for multiple polyploidy in olive tree relatives. Formation of tetraploids and hexaploids may have played a major role in the diversification of the olive complex in north-west Africa. The fact that polyploidy is found in narrow endemic subspecies from Madeira (subsp. cerasiformis) and the Agadir Mountains (subsp. maroccana) suggests that polyploidization has been favoured to overcome inbreeding depression. Lastly, based on previous phylogenetic analyses, we hypothesize that subsp. cerasiformis resulted from hybridization between ancestors

Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

Treesearch

Maria L. Zapiola; Richard C. Cronn; Carol A. Mallory-Smith

2010-01-01

We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape-level study of gene flow from transgenic gylphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of...

Identification and DUS Testing of Rice Varieties through Microsatellite Markers.

PubMed

Pourabed, Ehsan; Jazayeri Noushabadi, Mohammad Reza; Jamali, Seyed Hossein; Moheb Alipour, Naser; Zareyan, Abbas; Sadeghi, Leila

2015-01-01

Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests.

[Distribution of MICA microsatellite in 13 population groups of China].

PubMed

Ban, G H; Chu, J Y; Xu, S B; Yang, Z Q; Qian, Y P; Yu, J K; Na, J B; Liu, X J; Zhang, S Z

2001-01-01

The genetic data of MICA microsatellite were obtained by genotyping 577 samples in 13 population groups of China, which are Han-YN, Han-GD, Han-SD, Bai, Dai, Lahu, Li, Naxi, Sala, She, Tu, Wa and Zang-YN, with genescan. Five alleles have been observed in the population groups, which are A4, A5, A5.1, A6 and A9. A5 allele is the most frequent in all population groups except Lahu and Li, while the most frequent allele for Lahu and Li is A5. 1 and A4 respectively. The second most frequent allele is the A5.1 in Han-YN, Han-SD, Dai, Naxi, Sala, She, and Wa. The lest frequent allele for Han-YN, Han-GD, Lahu, Naxi, She, Wa is the A6 which is not observed in Li. A4 allele is the lest frequent in Han-SD, Bai, Dai, Sala, Tu, Zang-YN. The results show that the distribution of MICA microsatellite is different in these population groups, and the polymorphism information contents (PIC) of this microsatellite is high. It is a potential useful marker in the study of human origin and migration, personal identification, gene mapping and location, and disease diagnosis.

Identification and DUS Testing of Rice Varieties through Microsatellite Markers

PubMed Central

Pourabed, Ehsan; Jazayeri Noushabadi, Mohammad Reza; Jamali, Seyed Hossein; Moheb Alipour, Naser; Zareyan, Abbas; Sadeghi, Leila

2015-01-01

Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests. PMID:25755666

Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers.

PubMed

Moncada, Ximena; Pelsy, Frédérique; Merdinoglu, Didier; Hinrichsen, Patricio

2006-11-01

Intravarietal genetic diversification associated with geographical dispersal of a vegetatively propagated species was studied using grapevine Vitis vinifera L. 'Cabernet Sauvignon' as a model. Fifty-nine clonal samples obtained from 7 countries (France, Chile, Spain, Australia, Hungary, USA, and Italy) were analyzed using 84 microsatellite markers. Eighteen polymorphic microsatellite loci (21.4%) were detected, finding 22 different genotypes in the population analyzed with a genetic similarity of over 97%. The presence of chimeric clones was evidenced at locus VMC5g7 by means of a segregation analysis of descendants by self-pollination of a triallelic Chilean clone and by somatic embryogenesis analysis, showing a mutation in L2 cell layer. Only 2 clones (obtained from France and Australia) presented the ancestral genotype, and the most divergent genotype was exhibited by another French clone, which had accumulated 5 somatic mutations. The 2 largest populations considered (from France and Chile) showed a clear divergency in the polymorphisms detected. These antecedents enabled the tracing of geographical dispersal with a phylogenetic hypothesis supporting France as the center of origin of diversification of Cabernet Sauvignon. The results obtained could help to explain diversification processes in other grapevine cultivars. The possibility that this kind of genetic variability occurs in other vegetatively propagated species is discussed, focusing on possible fingerprinting applications.

DNA typing of Pakistani cattle breeds Tharparkar and Red Sindhi by microsatellite markers.

PubMed

Azam, Amber; Babar, Masroor Ellahi; Firyal, Sehrish; Anjum, Aftab Ahmad; Akhtar, Nabeela; Asif, Muhammad; Hussain, Tanveer

2012-02-01

Microsatellite markers are used for any individual identity and breed characterization in animals that is an efficient and successful way of investigation. They are used for multiple purposes as genetic detectors including, rapid mutation rate, high level of polymorphism, and range of variety of microsatellite markers available. A panel of 19 microsatellite markers was developed for breed characterization in Tharparkar and Red Sindhi breeds of cattle in Pakistan. Forty four blood samples of cattle (each breed) were collected from Department of Livestock Management, Sindh Agriculture University, Tandojam, Tando Qaiser, Tharparkar Cattle Farm Nabi sar Road, Umer Kot, Sindh, and Govt. Red Sindhi Cattle Breeding Farm, Tando Muhammad Khan Pakistan. Breed characterization was 100% successful. Average PIC, He and Power of Exclusion values were found to be 0.91, 0.62 and 13.28, respectively. Pattern of allelic frequencies of most of the microsatellite markers were clearly distinct between two breeds. As a result of present study a reliable, efficient and very informative panel of microsatellite markers was successfully developed which was capable to interpret individual identity, forensic cases and breed characterization in cattle. This facility is ready to be provided to local cattle breeder at commercial level for DNA testing of cattle. This study will also be highly helpful for breed conservation of cattle. In addition this study can also become a basis to open up new disciplines of animal forensics in Pakistan.

Complex distribution patterns, ecology and coexistence of ploidy levels of Allium oleraceum (Alliaceae) in the Czech Republic

PubMed Central

Duchoslav, Martin; Šafářová, Lenka; Krahulec, František

2010-01-01

Background and Aims Despite extensive study of polyploidy, its origin, and ecogeographical differences between polyploids and their diploid progenitors, few studies have addressed ploidy-level structure and patterns of ecogeographical differentiation at various spatial scales using detailed sampling procedures. The pattern of coexistence of polyploids in the geophyte Allium oleraceum at the landscape and locality scale and their ecology were studied. Methods Flow cytometry and root-tip squashes were used to identify the ploidy level of 4347 plants from 325 populations sampled from the Czech Republic using a stratified random sampling procedure. Ecological differentiation among ploidy levels was tested by comparing sets of environmental variables recorded at each locality. Key Results Across the entire sampling area, pentaploids (2n = 5x = 40) predominated, while hexaploids (2n = 6x = 48) and tetraploids (2n = 4x = 32) were less frequent. The distribution of tetra- and hexaploids was partially sympatric (in the eastern part) to parapatric (in the western part of the Czech Republic) whereas pentaploids were sympatric with other cytotypes. Plants of different ploidy levels were found to be ecologically differentiated and the ruderal character of cytotypes increased in the direction 4x → 5x → 6x with the largest realized niche differences between tetra- and hexaploids. Most populations contained only one ploidy level (77 %), 22 % had two (all possible combinations) and 1 % were composed of three ploidy levels. The majority of 4x + 5x and 5x + 6x mixed populations occurred in sympatry with uniform populations of the participating cytotypes in sites with ecologically heterogeneous or marginal environment, suggesting secondary contact between cytotypes. Some mixed 4x + 6x populations dominated by tetraploids being sympatric and intermixed with uniform 4x populations might represent primary zones of cytotype contact. Almost no mixed accessions were observed on the fine

Cacao single-nucleotide polymorphism (SNP) markers: A discovery strategy to identify SNPs for genotyping, genetic mapping and genome wide association studies (GWAS)

USDA-ARS?s Scientific Manuscript database

Single-nucleotide polymorphisms (SNPs) are the most common genetic markers in Theobroma cacao, occurring approximately once in every 200 nucleotides. SNPs, like microsatellites, are co-dominant and PCR-based, but they have several advantages over microsatellites. They are unambiguous, so that a SN...

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

PubMed Central

Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

2013-01-01

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

Development and characterization of polymorphic microsatellitemarkers for the crested caracara, Caracara cheriway

USGS Publications Warehouse

Vaughn, Erin E.; Dwyer, James F.; Morrison, Joan L.; Culver, Melanie

2015-01-01

We isolated novel microsatellites from the crested caracara (Caracara cheriway) with a shotgun pyrosequencing approach. We tested 80 loci for polymorphism among 20 individuals from the threatened Florida population. Fourteen loci were polymorphic. The mean number of alleles was 2.21 (range 2–3) and the mean observed heterozygosity was 0.41 (range 0.15–0.65). None of the 14 polymorphic loci exhibited significant linkage disequilibrium nor did they deviate significantly from Hardy–Weinberg expectations. We also report 16 monomorphic loci.

Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene

PubMed Central

2008-01-01

Background The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5' flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5' flanking region of AVPR1A contains a tandem duplication of two ~350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT)25 microsatellite; the second block, DupB, has a complex (CT)4-(TT)-(CT)8-(GT)24 polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in

Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene.

PubMed

Donaldson, Zoe R; Kondrashov, Fyodor A; Putnam, Andrea; Bai, Yaohui; Stoinski, Tara L; Hammock, Elizabeth A D; Young, Larry J

2008-06-23

The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5' flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5' flanking region of AVPR1A contains a tandem duplication of two approximately 350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT)25 microsatellite; the second block, DupB, has a complex (CT)4-(TT)-(CT)8-(GT)24 polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a

Identification and characterization of 43 microsatellite markers derived from expressed sequence tags of the sea cucumber ( Apostichopus japonicus)

NASA Astrophysics Data System (ADS)

Jiang, Qun; Li, Qi; Yu, Hong; Kong, Lingfeng

2011-06-01

The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from Gen-Bank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles, and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species.

A panel of ten microsatellite loci for the Chagas disease vector Rhodnius prolixus (Hemiptera: Reduviidae).

PubMed

Fitzpatrick, S; Watts, P C; Feliciangeli, M D; Miles, M A; Kemp, S J

2009-03-01

Rhodnius prolixus is the main vector of Chagas disease in Venezuela, where it is found colonising rural housing consisting of unplastered adobe walls with palm and/or metal roofs. Vector control failure in Venezuela may be due to the invasion of houses by silvatic populations of R. prolixus found in palms. As part of a study to determine if domestic and silvatic populations of R. prolixus are isolated, thus clarifying the role of silvatic populations in maintaining house infestations, we constructed three partial genomic microsatellite libraries. A panel of ten dinucleotide polymorphic microsatellite markers was selected for genotyping. Allele numbers per locus ranged from three to twelve, with observed and expected heterozygosity ranging from 0.26 to 0.55 and 0.32 to 0.66. The microsatellite markers presented here will contribute to the control of Chagas disease in Venezuela and Colombia through the provision of population information that may allow the design of improved control strategies.

Isolation and characterization of chromosome-gain and increase-in-ploidy mutants in yeast.

PubMed

Chan, C S; Botstein, D

1993-11-01

We have developed a colony papillation assay for monitoring the copy number of genetically marked chromosomes II and III in Saccharomyces cerevisiae. The unique feature of this assay is that it allows detection of a gain of the marked chromosomes even if there is a gain of the entire set of chromosomes (increase-in-ploidy). This assay was used to screen for chromosome-gain or increase-in-ploidy mutants. Five complementation groups have been defined for recessive mutations that confer an increase-in-ploidy (ipl) phenotype, which, in each case, cosegregates with a temperature-sensitive growth phenotype. Four new alleles of CDC31, which is required for spindle pole body duplication, were also recovered from this screen. Temperature-shift experiments with ipl1 cells show that they suffer severe nondisjunction at 37 degrees. Similar experiments with ipl2 cells show that they gain entire sets of chromosomes and become arrested as unbudded cells at 37 degrees. Molecular cloning and genetic mapping show that IPL1 is a newly identified gene, whereas IPL2 is allelic to BEM2, which is required for normal bud growth.

Isolation and Characterization of Chromosome-Gain and Increase-in-Ploidy Mutants in Yeast

PubMed Central

Chan, CSM.; Botstein, D.

1993-01-01

We have developed a colony papillation assay for monitoring the copy number of genetically marked chromosomes II and III in Saccharomyces cerevisiae. The unique feature of this assay is that it allows detection of a gain of the marked chromosomes even if there is a gain of the entire set of chromosomes (increase-in-ploidy). This assay was used to screen for chromosome-gain or increase-in-ploidy mutants. Five complementation groups have been defined for recessive mutations that confer an increase-in-ploidy (ipl) phenotype, which, in each case, cosegregates with a temperature-sensitive growth phenotype. Four new alleles of CDC31, which is required for spindle pole body duplication, were also recovered from this screen. Temperature-shift experiments with ipl1 cells show that they suffer severe nondisjunction at 37°. Similar experiments with ipl2 cells show that they gain entire sets of chromosomes and become arrested as unbudded cells at 37°. Molecular cloning and genetic mapping show that IPL1 is a newly identified gene, whereas IPL2 is allelic to BEM2, which is required for normal bud growth. PMID:8293973

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

PubMed Central

Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S.; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C.L.L.; Singh, Sube; Jain, Mukesh; Tyagi, Akhilesh K.; Parida, Swarup K.

2013-01-01

We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5′ untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication. PMID:23633531

Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna

PubMed Central

Nikolic, Natacha; Duthoy, Stéphanie; Destombes, Antoine; Bodin, Nathalie; West, Wendy; Puech, Alexis; Bourjea, Jérôme

2015-01-01

Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01

Microsatellite markers characterized in the barn owl (Tyto alba) and of high utility in other owls (Strigiformes: AVES).

PubMed

Klein, Akos; Horsburgh, Gavin J; Küpper, Clemens; Major, Agnes; Lee, Patricia L M; Hoffmann, Gyula; Mátics, Róbert; Dawson, Deborah A

2009-11-01

We have identified 15 polymorphic microsatellite loci for the barn owl (Tyto alba), five from testing published owl loci and 10 from testing non-owl loci, including loci known to be of high utility in passerines and shorebirds. All 15 loci were sequenced in barn owl, and new primer sets were designed for eight loci. The 15 polymorphic loci displayed two to 26 alleles in 56-58 barn owls. When tested in 10 other owl species (n = 1-6 individuals), between four and nine loci were polymorphic per species. These loci are suitable for studies of population structure and parentage in owls. © 2009 Blackwell Publishing Ltd.

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

Treesearch

Craig S. Echt; Surya Saha; Konstantin V. Krutovsky; Kokulapalan Wimalanathan; John E. Erpelding; Chun Liang; C Dana Nelson

2011-01-01

Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety...

Detecting and Removing Ascertainment Bias in Microsatellites from the HGDP-CEPH Panel

PubMed Central

Eriksson, Anders; Manica, Andrea

2011-01-01

Although ascertainment bias in single nucleotide polymorphisms is a well-known problem, it is generally accepted that microsatellites have mutation rates too high for bias to be a concern. Here, we analyze in detail the large set of microsatellites typed for the Human Genetic Diversity Panel (HGDP)-CEPH panel. We develop a novel framework based on rarefaction to compare heterozygosity across markers with different mutation rates. We find that, whereas di- and tri-nucleotides show similar patterns of within- and between-population heterozygosity, tetra-nucleotides are inconsistent with the other two motifs. In addition, di- and tri-nucleotides are consistent with 16 unbiased tetra-nucleotide markers, whereas the HPGP-CEPH tetra-nucleotides are significantly different. This discrepancy is due to the HGDP-CEPH tetra-nucleotides being too homogeneous across Eurasia, even after their slower mutation rate is taken into account by rarefying the other markers. The most likely explanation for this pattern is ascertainment bias. We strongly advocate the exclusion of tetra-nucleotides from future population genetics analysis of this dataset, and we argue that other microsatellite datasets should be investigated for the presence of bias using the approach outlined in this article. PMID:22384358

Atypical ploidy cycles, Spo11, and the evolution of meiosis.

PubMed

Bloomfield, Gareth

2016-06-01

The Spo11 protein induces DNA double strand breaks before the first division of meiosis, enabling the formation of the chiasmata that physically link homologous chromosomes as they align. Spo11 is an ancient and well conserved protein, related in sequence and structure to a DNA topoisomerase subunit found in Archaea as well as a subset of eukaryotes. However the origins of its meiotic function are unclear. This review examines some apparent exceptions to the rule that Spo11 activity is specific to, and required for meiosis. Spo11 appears to function in the context of unusual forms of ploidy reduction in some protists and fungi. One lineage of amoebae, the dictyostelids, is thought to undergo meiosis during its sexual cycle despite having lost Spo11 entirely. Further experimental characterisation of these and other non-canonical ploidy cycling mechanisms may cast light of the evolution of meiosis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of highly informative cross-species microsatellite panels for the Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) including five novel primers

USGS Publications Warehouse

Hunter, Margaret Kellogg; Broderick, Damien; Ovenden, Jennifer R.; Tucker, Kimberly Pause; Bonde, Robert K.; McGuire, Peter M.; Lanyon, Janet M.

2010-01-01

The Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) are threatened species of aquatic mammals in the order Sirenia. Sirenian conservation and management actions would benefit from a more complete understanding of genetic diversity and population structure. Generally, species-specific microsatellite markers are employed in conservation genetic studies; however, robust markers can be difficult and costly to isolate. To increase the number of available markers, dugong and manatee microsatellite primers were evaluated for cross-species amplification. Furthermore, one manatee and four dugong novel primers are reported. After polymerase chain reaction optimization, 23 (92%) manatee primers successfully amplified dugong DNA, of which 11 (48%) were polymorphic. Of the 32 dugong primers tested, 27 (84%) yielded product in the manatee, of which 17 (63%) were polymorphic. Dugong and manatee primers were compared and the most informative markers were selected to create robust and informative marker-panels for each species. These crossspecies microsatellite marker-panels can be employed to assess other sirenian populations and can provide beneficial information for the protection and management of these unique mammals.

Isolation and characterization of microsatellite markers for Cotinus coggygria Scop. (Anacardiaceae) by 454 pyrosequencing.

PubMed

Wang, Wei; Li, Zhuo; Li, Yong

2014-03-24

Cotinus coggygria Scop. (Anacardiaceae) is a deciduous shrub or small tree that is native to a large area covering from southern Europe, east across central Asia, and the Himalayas in northern China. Shotgun 454 pyrosequencing was used to develop microsatellite markers from the genome of C. coggygria. In this study, 349 microsatellite loci were identified from 40,074 individual sequence reads produced by one-sixteenth run, and primer pairs were designed for these loci. To test the primer amplification efficiency, 50 microsatellite primer pairs were tested across 12 individuals from two C. coggygria populations (Wuzhi Mountain: 36°30'N, 113°39'E; Tianlong Mountain: 37°42'N, 112°26'E). Among the 50 tested primer pairs, eight were found to be polymorphic. The average allele number of the microsatellites was 3.5 per locus, with a range from two to five. The inbreeding coefficient ranged from -0.478 to 0.222. The observed and expected heterozygosities varied from 0.167 to 0.750 and from 0.163 to 0.743, respectively. This set of markers is potentially useful for assessing the genetic diversity, as well as for understanding the population structure and phylogeographical and landscape genetic patterns, of C. coggygria.

Microsatellite markers for the native Texas perennial grass, Panicum hallii (Poaceae).

PubMed

Lowry, David B; Purmal, Colin T; Meyer, Eli; Juenger, Thomas E

2012-03-01

We developed microsatellites for Panicum hallii for studies of gene flow, population structure, breeding experiments, and genetic mapping. Next-generation (454) genomic sequence data were used to design markers. Eighteen robust markers were discovered, 15 of which were polymorphic across six accessions of P. hallii var. hallii. Fourteen of the markers cross-amplified in a P. capillare accession. For the 15 polymorphic markers, the total number of alleles per locus ranged from two to 26 (mean: 11.0) across six populations (11-19 individuals per population). Observed heterozygosity (mean: 0.031) was 13.7 times lower than the expected heterozygosity (mean: 0.426). The deficit of heterozygous individuals is consistent with P. hallii having a high rate of self-fertilization. These markers will be useful for studies in P. hallii and related species.

Development of microsatellite loci exhibiting reverse ascertainment bias and a sexing marker for use in Emperor Geese (Chen canagica)

USGS Publications Warehouse

Gravley, Megan C.; Sage, George K.; Schmutz, Joel A.; Talbot, Sandra L.

2017-01-01

The Alaskan population of Emperor Geese (Chen canagica) nests on the Yukon–Kuskokwim Delta in western Alaska. Numbers of Emperor Geese in Alaska declined from the 1960s to the mid-1980s and since then, their numbers have slowly increased. Low statistical power of microsatellite loci developed in other waterfowl species and used in previous studies of Emperor Geese are unable to confidently assign individual identity. Microsatellite loci for Emperor Goose were therefore developed using shotgun amplification and next-generation sequencing technology. Forty-one microsatellite loci were screened and 14 were found to be polymorphic in Emperor Geese. Only six markers – a combination of four novel loci and two loci developed in other waterfowl species – are needed to identify an individual from among the Alaskan Emperor Goose population. Genetic markers for identifying sex in Emperor Geese were also developed. The 14 novel variable loci and 15 monomorphic loci were screened for polymorphism in four other Arctic-nesting goose species, Black Brant (Branta bernicla nigricans), Greater White-fronted (Anser albifrons), Canada (B. canadensis) and Cackling (B. hutchinsii) Goose. Emperor Goose exhibited the smallest average number of alleles (3.3) and the lowest expected heterozygosity (0.467). Greater White-fronted Geese exhibited the highest average number of alleles (4.7) and Cackling Geese the highest expected heterozygosity (0.599). Six of the monomorphic loci were variable and able to be characterised in the other goose species assayed, a predicted outcome of reverse ascertainment bias. These findings fail to support the hypothesis of ascertainment bias due to selection of microsatellite markers.

Prognostic significance of DNA ploidy in adenocarcinoma of the pancreas. A flow cytometric study of paraffin-embedded specimens.

PubMed

Porschen, R; Remy, U; Bevers, G; Schauseil, S; Hengels, K J; Borchard, F

1993-06-15

The prognostic significance of tumor DNA ploidy in patients with cancer of the pancreas has not been defined because conflicting results have been reported. DNA content was measured in 56 ductal adenocarcinomas of the pancreas. DNA ploidy status was evaluated by flow cytometry in nuclei isolated from paraffin-embedded tumor tissues. An abnormal DNA stemline was observed in 27 (48%) patients. The percentage of aneuploid tumors was significantly increased in tumors classified as Stage III/IV (53%) compared with those classified as Stage I (22%). A borderline significant association existed between DNA ploidy and radicality of surgery (P = 0.08). The median survival of patients with diploid carcinomas was 6.9 months (standard error, +/- 0.9) in comparison to 4.5 +/- 1.2 months for patients with aneuploid tumors (P = 0.013 by generalized Wilcoxon test; P = 0.023 by generalized Savage test). Although a selection bias cannot be excluded, survival of patients with a radical resection was longer than that of patients with a nonradical resection (P = 0.0008 and P = 0.0085, respectively). In addition, presence of distant metastasis (P = 0.0006 [Wilcoxon test] and P = 0.033 [Savage test]) could be identified as a prognostic factor. In a Cox regression model, results of surgery and DNA ploidy were independent prognostic variables. Because DNA ploidy has a significant impact on prognosis in pancreatic cancer, it should be used as a variable for stratified randomization of patients in therapeutic trials.

Levels of Intra-specific AFLP Diversity in Tuber-Bearing Potato Species with Different Breeding Systems and Ploidy Levels

PubMed Central

Bryan, Glenn J.; McLean, Karen; Waugh, Robbie; Spooner, David M.

2017-01-01

DNA-based marker analysis of plant genebank material has become a useful tool in the evaluation of levels of genetic diversity and for the informed use and maintenance of germplasm. In this study, we quantify levels of amplified fragment length polymorphism (AFLP) in representative accessions of wild and cultivated potato species of differing geographic origin, ploidy, and breeding system. We generated 449 polymorphic AFLP fragments in 619 plants, representing multiple plants (16–23) from 17 accessions of 14 potato taxa as well as single plants sampled from available accessions (from 3 to 56) of the same 14 taxa. Intra-accession diversities were compared to those of a synthetic ‘taxon-wide’ population comprising a single individual from a variable number of available accessions of each sampled taxon. Results confirm the expected considerably lower levels of polymorphism within accessions of self-compatible as compared to self-incompatible taxa. We observed broadly similar levels of ‘taxon-wide’ polymorphism among self-compatible and self-incompatible species, with self-compatible taxa showing only slightly lower rates of polymorphism. The most diverse accessions were the two cultivated potato accessions examined, the least diverse being the Mexican allohexaploids Solanum demissum and S. iopetalum. Generally allopolyploid self-compatible accessions exhibited lower levels of diversity. Some purported self-incompatible accessions showed relatively low levels of marker diversity, similar to the more diverse self-compatible material surveyed. Our data indicate that for self-compatible species a single plant is highly representative of a genebank accession. The situation for self-incompatible taxa is less clear, and sampling strategies used will depend on the type of investigation. These results have important implications for those seeking novel trait variation (e.g., disease resistance) in gene banks as well as for the selection of individuals for genomics

[Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka].

PubMed

Khrustaleva, A M; Volkov, A A; Stoklitskaia, D S; Miuge, N S; Zelenina, D A

2010-11-01

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.

Microsatellite markers for the Pilosella alpicola group (Hieraciinae, Asteraceae) and their cross-amplification in other Hieraciinae genera.

PubMed

Vít, Petr; Šingliarová, Barbora; Zozomová-Lihová, Judita; Marhold, Karol; Krak, Karol

2015-08-01

Microsatellite markers were developed for the Pilosella alpicola group (Asteraceae), comprising four closely related species distributed in subalpine areas of Europe. These species are believed to have diverged recently, but display contrasting cytogeographic patterns and variation in breeding systems, representing a promising model system for studying plant speciation, adaptation, and recent polyploidization. We developed 17 microsatellite markers for the P. alpicola group using 454 sequencing. Sixteen markers were polymorphic, with the number of alleles per locus ranging from seven to 16 and observed and expected heterozygosity ranging from 0.45 to 0.84 and 0.72 to 0.92, respectively. Ten and five loci amplified in the related species, P. echioides and P. officinarum, respectively, but only two in Andryala and one in Hieracium s. str. The developed microsatellite markers have high potential to become useful tools to study microevolutionary processes in the P. alpicola group and related Pilosella species.

Geographic Variation in Festuca rubra L. Ploidy Levels and Systemic Fungal Endophyte Frequencies.

PubMed

Dirihan, Serdar; Helander, Marjo; Väre, Henry; Gundel, Pedro E; Garibaldi, Lucas A; Irisarri, J Gonzalo N; Saloniemi, Irma; Saikkonen, Kari

2016-01-01

Polyploidy and symbiotic Epichloë fungal endophytes are common and heritable characteristics that can facilitate environmental range expansion in grasses. Here we examined geographic patterns of polyploidy and the frequency of fungal endophyte colonized plants in 29 Festuca rubra L. populations from eight geographic sites across latitudes from Spain to northernmost Finland and Greenland. Ploidy seemed to be positively and negatively correlated with latitude and productivity, respectively. However, the correlations were nonlinear; 84% of the plants were hexaploids (2n = 6x = 42), and the positive correlation between ploidy level and latitude is the result of only four populations skewing the data. In the southernmost end of the gradient 86% of the plants were tetraploids (2n = 4x = 28), whereas in the northernmost end of the gradient one population had only octoploid plants (2n = 8x = 56). Endophytes were detected in 22 out of the 29 populations. Endophyte frequencies varied among geographic sites, and populations and habitats within geographic sites irrespective of ploidy, latitude or productivity. The highest overall endophyte frequencies were found in the southernmost end of the gradient, Spain, where 69% of plants harbored endophytes. In northern Finland, endophytes were detected in 30% of grasses but endophyte frequencies varied among populations from 0% to 75%, being higher in meadows compared to riverbanks. The endophytes were detected in 36%, 30% and 27% of the plants in Faroe Islands, Iceland and Switzerland, respectively. Practically all examined plants collected from southern Finland and Greenland were endophyte-free, whereas in other geographic sites endophyte frequencies were highly variable among populations. Common to all populations with high endophyte frequencies is heavy vertebrate grazing. We propose that the detected endophyte frequencies and ploidy levels mirror past distribution history of F. rubra after the last glaciation period, and local

Geographic Variation in Festuca rubra L. Ploidy Levels and Systemic Fungal Endophyte Frequencies

PubMed Central

Dirihan, Serdar; Helander, Marjo; Väre, Henry; Gundel, Pedro E.; Garibaldi, Lucas A.; Irisarri, J. Gonzalo N.; Saloniemi, Irma; Saikkonen, Kari

2016-01-01

Polyploidy and symbiotic Epichloë fungal endophytes are common and heritable characteristics that can facilitate environmental range expansion in grasses. Here we examined geographic patterns of polyploidy and the frequency of fungal endophyte colonized plants in 29 Festuca rubra L. populations from eight geographic sites across latitudes from Spain to northernmost Finland and Greenland. Ploidy seemed to be positively and negatively correlated with latitude and productivity, respectively. However, the correlations were nonlinear; 84% of the plants were hexaploids (2n = 6x = 42), and the positive correlation between ploidy level and latitude is the result of only four populations skewing the data. In the southernmost end of the gradient 86% of the plants were tetraploids (2n = 4x = 28), whereas in the northernmost end of the gradient one population had only octoploid plants (2n = 8x = 56). Endophytes were detected in 22 out of the 29 populations. Endophyte frequencies varied among geographic sites, and populations and habitats within geographic sites irrespective of ploidy, latitude or productivity. The highest overall endophyte frequencies were found in the southernmost end of the gradient, Spain, where 69% of plants harbored endophytes. In northern Finland, endophytes were detected in 30% of grasses but endophyte frequencies varied among populations from 0% to 75%, being higher in meadows compared to riverbanks. The endophytes were detected in 36%, 30% and 27% of the plants in Faroe Islands, Iceland and Switzerland, respectively. Practically all examined plants collected from southern Finland and Greenland were endophyte-free, whereas in other geographic sites endophyte frequencies were highly variable among populations. Common to all populations with high endophyte frequencies is heavy vertebrate grazing. We propose that the detected endophyte frequencies and ploidy levels mirror past distribution history of F. rubra after the last glaciation period, and local

Development and characterization of microsatellite markers for the Pacific abalone ( Haliotis discus) via EST database mining

NASA Astrophysics Data System (ADS)

Zhan, Aibin; Bao, Zhenmin; Wang, Mingling; Chang, Dan; Yuan, Jian; Wang, Xiaolong; Hu, Xiaoli; Liang, Chengzhu; Hu, Jingjie

2008-05-01

The EST database of the Pacific abalone ( Haliotis discus) was mined for developing microsatellite markers. A total of 1476 EST sequences were registered in GenBank when data mining was performed. Fifty sequences (approximately 3.4%) were found to contain one or more microsatellites. Based on the length and GC content of the flanking regions, cluster analysis and BLASTN, 13 microsatellite-containing ESTs were selected for PCR primer design. The results showed that 10 out of 13 primer pairs could amplify scorable PCR products and showed polymorphism. The number of alleles ranged from 2 to 13 and the values of H o and H e varied from 0.1222 to 0.8611 and 0.2449 to 0.9311, respectively. No significant linkage disequilibrium (LD) between any pairs of these loci was found, and 6 of 10 loci conformed to the Hardy-Weinberg equilibrium (HWE). These EST-SSRs are therefore potential tools for studies of intraspecies variation and hybrid identification.

Analysis of genetic diversity of Chinese dairy goats via microsatellite markers.

PubMed

Wang, G Z; Chen, S S; Chao, T L; Ji, Z B; Hou, L; Qin, Z J; Wang, J M

2017-05-01

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

Polymorphisms of the Tissue Inhibitor of Metalloproteinase 3 Gene Are Associated with Resistance to High-Altitude Pulmonary Edema (HAPE) in a Japanese Population: A Case Control Study Using Polymorphic Microsatellite Markers

PubMed Central

Kobayashi, Nobumitsu; Hanaoka, Masayuki; Droma, Yunden; Ito, Michiko; Katsuyama, Yoshihiko; Kubo, Keishi; Ota, Masao

2013-01-01

Introduction High-altitude pulmonary edema (HAPE) is a hypoxia-induced, life-threatening, high permeability type of edema attributable to pulmonary capillary stress failure. Genome-wide association analysis is necessary to better understand how genetics influence the outcome of HAPE. Materials and Methods DNA samples were collected from 53 subjects susceptible to HAPE (HAPE-s) and 67 elite Alpinists resistant to HAPE (HAPE-r). The genome scan was carried out using 400 polymorphic microsatellite markers throughout the whole genome in all subjects. In addition, six single nucleotide polymorphisms (SNPs) of the gene encoding the tissue inhibitor of metalloproteinase 3 (TIMP3) were genotyped by Taqman® SNP Genotyping Assays. Results The results were analyzed using case-control comparisons. Whole genome scanning revealed that allele frequencies in nine markers were statistically different between HAPE-s and HAPE-r subjects. The SNP genotyping of the TIMP3 gene revealed that the derived allele C of rs130293 was associated with resistance to HAPE [odds ratio (OR) = 0.21, P = 0.0012) and recessive inheritance of the phenotype of HAPE-s (P = 0.0012). A haplotype CAC carrying allele C of rs130293 was associated with resistance to HAPE. Discussion This genome-wide association study revealed several novel candidate genes associated with susceptibility or resistance to HAPE in a Japanese population. Among those, the minor allele C of rs130293 (C/T) in the TIMP3 gene was linked to resistance to HAPE; while, the ancestral allele T was associated with susceptibility to HAPE. PMID:23991023

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

PubMed Central

Aranguren-Méndez, José; Jordana, Jordi; Gomez, Mariano

2001-01-01

Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

Bridging the Gap Between Large-scale Data Sets and Analyses: Semi-automated Methods to Facilitate Length Polymorphism Scoring and Data Analyses.

EPA Science Inventory

Amplified fragment length polymorphism (AFLP) markers can be developed more quickly and at a lower cost than microsatellite and single nucleotide polymorphism markers, which makes them ideal markers for large-scale studies of understudied taxa — such as species at risk. However,...

Microsatellite markers for the endangered Roanoke logperch, Percina rex (Percidae) and their potential utility for other darter species

USGS Publications Warehouse

Dutton, D.J.; Roberts, J.H.; Angermeier, P.L.; Hallerman, E.M.

2008-01-01

The Roanoke logperch (Percina rex Jordan and Evermann), an endangered fish, occurs in only six watersheds in the Roanoke and Chowan river drainages of Virginia, USA. The species' population genetic structure is poorly known. We developed 16 microsatellite markers that were reliably scorable and polymorphic P. rex. Markers were also screened in seven other darter species of the genus Percina. Most markers exhibited successful amplification and polymorphism in several species. These markers may therefore prove useful for population genetic studies in other darters, a diverse but highly imperiled group. ?? 2008 The Authors.

Characterization of ten microsatellite loci in the Broad-tailed hummingbird (Selasphorus platycercus)

USGS Publications Warehouse

Oyler-McCance, Sara J.; Fike, Jennifer A.; Talley-Farnham, Tiffany; Engelman, Tena; Engelman, Fred

2011-01-01

The Broad-tailed Hummingbird (Selaphorus platycercus) breeds at higher elevations in the central and southern Rockies, eastern California, and Mexico and has been studied for 8 years in Rocky Mountain National Park, Colorado. Questions regarding the relatedness of Broad-tailed Hummingbirds banded together and then recaptured in close time proximity in later years led us to isolate and develop primers for 10 polymorphic microsatellite loci. In a screen of 25 individuals from a population in Rocky Mountain National Park, the 10 loci were found to have levels of variability ranging from two to 16 alleles. No loci were found to depart from linkage disequilibrium, although two loci revealed significant departures from Hardy–Weinberg equilibrium. These 10 microsatellite loci will be applicable for population genetic analyses, investigation of mating systems and relatedness, and may help gain insight into the migration timing and routes for this species.

Development of MHC-Linked Microsatellite Markers in the Domestic Cat and Their Use to Evaluate MHC Diversity in Domestic Cats, Cheetahs, and Gir Lions

PubMed Central

Morris, Katrina M.; Kirby, Katherine; Beatty, Julia A.; Barrs, Vanessa R.; Cattley, Sonia; David, Victor; O’Brien, Stephen J.; Menotti-Raymond, Marilyn

2014-01-01

Diversity within the major histocompatibility complex (MHC) reflects the immunological fitness of a population. MHC-linked microsatellite markers provide a simple and an inexpensive method for studying MHC diversity in large-scale studies. We have developed 6 MHC-linked microsatellite markers in the domestic cat and used these, in conjunction with 5 neutral microsatellites, to assess MHC diversity in domestic mixed breed (n = 129) and purebred Burmese (n = 61) cat populations in Australia. The MHC of outbred Australian cats is polymorphic (average allelic richness = 8.52), whereas the Burmese population has significantly lower MHC diversity (average allelic richness = 6.81; P < 0.01). The MHC-linked microsatellites along with MHC cloning and sequencing demonstrated moderate MHC diversity in cheetahs (n = 13) and extremely low diversity in Gir lions (n = 13). Our MHC-linked microsatellite markers have potential future use in diversity and disease studies in other populations and breeds of cats as well as in wild felid species. PMID:24620003

Microsatellite variation and rare alleles in a bottlenecked Hawaiian Islands endemic: implications for reintroductions

USGS Publications Warehouse

Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Seixas, Pedro P.; Courtot, Karen

2015-01-01

Conservation of genetic biodiversity in endangered wildlife populations is an important challenge to address since the loss of alleles and genetic drift may influence future adaptability. Reintroduction aims to re-establish species to restored or protected ecosystems; however, moving a subset of individuals may result in loss of gene variants during the management-induced bottleneck (i.e. translocation). The endangered Laysan teal Anas laysanensis was once widespread across the Hawaiian archipelago, but became isolated on Laysan Island (415 ha) from the mid-1800s until 2004 when a translocation to Midway Atoll (596 ha) was undertaken to reduce extinction risks. We compared genetic diversity and quantified variation at microsatellite loci sampled from 230 individuals from the wild populations at Laysan (1999 to 2009) and Midway (2007 to 2010; n = 133 Laysan, n = 96 Midway birds). We identified polymorphic markers by screening nuclear microsatellites (N = 83). Low nuclear variation was detected, consistent with the species’ insular isolation and historical bottleneck. Six of 83 microsatellites were polymorphic. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within populations. However, 2 rare alleles found in the Laysan source population were not present in Midway’s reintroduced population, and a unique allele was discovered in an individual on Midway. Differentiation between island populations was low (FST = 0.6%), but statistically significant. Our results indicate that genetic drift had little effect on offspring generations 3 to 6 yr post-release and demonstrate the utility of using known founder events to help quantify genetic capture during translocations and to inform management decisions.

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

PubMed Central

Moges, Asmare D.; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R.

2016-01-01

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia. PMID:26978654

cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications.

PubMed

Wani, Gowher A; Shah, Manzoor A; Reshi, Zafar A; Atangana, Alain R; Khasa, Damase P

2014-07-01

A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation.

Characterization of highly informative cross-species microsatellite panels for the Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) including five novel primers.

PubMed

Hunter, Margaret Kellogg; Broderick, Damien; Ovenden, Jennifer R; Tucker, Kimberly Pause; Bonde, Robert K; McGuire, Peter M; Lanyon, Janet M

2010-03-01

The Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) are threatened species of aquatic mammals in the order Sirenia. Sirenian conservation and management actions would benefit from a more complete understanding of genetic diversity and population structure. Generally, species-specific microsatellite markers are employed in conservation genetic studies; however, robust markers can be difficult and costly to isolate. To increase the number of available markers, dugong and manatee microsatellite primers were evaluated for cross-species amplification. Furthermore, one manatee and four dugong novel primers are reported. After polymerase chain reaction optimization, 23 (92%) manatee primers successfully amplified dugong DNA, of which 11 (48%) were polymorphic. Of the 32 dugong primers tested, 27 (84%) yielded product in the manatee, of which 17 (63%) were polymorphic. Dugong and manatee primers were compared and the most informative markers were selected to create robust and informative marker-panels for each species. These cross-species microsatellite marker-panels can be employed to assess other sirenian populations and can provide beneficial information for the protection and management of these unique mammals. Published 2009. This article is a US Government work and is in the public domain in the USA.

Isolation and characterization of 16 microsatellite loci in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae: Scolytinae)

Treesearch

C. S. Davis; K. E. Mock; B. J. Bentz; S. M. Bromilow; N. V. Bartell; B. W. Murray; A. D. Roe; J. E. K. Cooke

2009-01-01

We isolated 16 polymorphic microsatellite loci in the mountain pine beetle (Dendroctonus ponderosae Hopkins) and developed conditions for amplifying these markers in four multiplex reactions. Three to 14 alleles were detected per locus across two sampled populations. Observed and expected heterozygosities ranged from 0.000 to 0.902 and from 0.100 to 0.830, respectively...

Intraspecific ploidy variation: A hidden, minor player in plant-soil-mycorrhizal fungi interactions.

PubMed

Sudová, Radka; Pánková, Hana; Rydlová, Jana; Münzbergová, Zuzana; Suda, Jan

2014-01-01

Genome duplication and arbuscular mycorrhizal (AM) symbiosis are ubiquitous in angiosperms. While the significance of each of these phenomena separately has been intensively studied, their interaction remains to be understood. Three diploid and three hexaploid populations of Aster amellus (Asteraceae) were characterized in terms of the soil conditions in situ and mycorrhizal root colonization. In a greenhouse experiment, the effects of ploidy level, substrate conditions, and AM fungi on plant performance were then separated by growing noninoculated plants or plants inoculated with AM fungi in substrates native to either the diploids or hexaploids. The diploids inhabited nutritionally richer sites but did not differ from hexaploid plants in the level of mycorrhizal root colonization in situ. In the experiment, hexaploids generally performed better than the diploids. This intercytotype growth difference was enhanced by soil fertility, with hexaploids benefiting more from nutritionally richer substrate than the diploids. AM inoculation was crucial for plant growth and phosphorus uptake. The interaction between ploidy level and AM inoculation significantly influenced only dry mass of roots, phosphorus concentrations in shoot biomass, and the length of the extraradical mycelium in the nonsterile substrates. Our results support the idea that polyploidy can affect the mycorrhizal growth response of host plants. Nevertheless, the effects of the interaction between ploidy and inoculation were weaker than the main effects of these factors.

Development and Characterization of Microsatellite Markers for the Cape Gooseberry Physalis peruviana

PubMed Central

Simbaqueba, Jaime; Sánchez, Pilar; Sanchez, Erika; Núñez Zarantes, Victor Manuel; Chacon, Maria Isabel; Barrero, Luz Stella; Mariño-Ramírez, Leonardo

2011-01-01

Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species. PMID:22039540

Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana.

PubMed

Simbaqueba, Jaime; Sánchez, Pilar; Sanchez, Erika; Núñez Zarantes, Victor Manuel; Chacon, Maria Isabel; Barrero, Luz Stella; Mariño-Ramírez, Leonardo

2011-01-01

Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.

Development and characterization of thirteen microsatellite loci in Clark's nutcracker (Nucifraga columbiana)

USGS Publications Warehouse

Oyler-McCance, Sara J.; Fike, Jennifer A.; Castoe, Todd A.; Tomback, Diana F.; Wunder, Michael B.; Schaming, Taza D.

2013-01-01

Clark’s nutcrackers are important seed dispersers for two widely-distributed western North American conifers, whitebark pine and limber pine, which are declining due to outbreaks of mountain pine beetle and white pine blister rust. Because nutcracker seed dispersal services are key to maintaining viable populations of these imperiled pines, knowledge of movement patterns of Clark’s nutcrackers helps managers understand local extinction risks for these trees. To investigate population structure within Clark’s nutcracker, we developed primers for and characterized 13 polymorphic microsatellite loci. In a screen of 22 individuals from one population, levels of variability ranged from 6 to 15 alleles. No loci were found to be linked, although 4 loci revealed significant departures from Hardy–Weinberg equilibrium and evidence of null alleles. These microsatellite loci will enable population genetic analyses of Clark’s nutcrackers, which could provide insights into the spatial relationships between nutcrackers and the trees they help disperse.

Towards resolving the Knautia arvensis agg. (Dipsacaceae) puzzle: primary and secondary contact zones and ploidy segregation at landscape and microgeographic scales

PubMed Central

Kolář, Filip; Štech, Milan; Trávníček, Pavel; Rauchová, Jana; Urfus, Tomáš; Vít, Petr; Kubešová, Magdalena; Suda, Jan

2009-01-01

Background and Aims Detailed knowledge of variations in ploidy levels and their geographic distributions is one of the key tasks faced in polyploid research in natural systems. Flow cytometry has greatly facilitated the field of cytogeography by allowing characterization of ploidy levels at both the regional and population scale, and at multiple stages of the life cycle. In the present study, flow cytometry was employed to investigate the patterns and dynamics of ploidy variation in the taxonomically challenging complex Knautia arvensis (Dipsacaceae) and some of its allies (K. dipsacifolia, K. slovaca) in Central Europe. Methods DNA ploidy levels were estimated by DAPI flow cytometry in 5205 adult plants, 228 seedlings and 400 seeds collected from 292 Knautia populations in seven European countries. The flow cytometric data were supplemented with conventional chromosome counts. A subset of 79 accessions was subjected to estimation of the absolute genome size using propidium iodide flow cytometry. Key Results and Conclusions Five different ploidy levels (from 2x to 6x) were found, with triploids of K. arvensis being recorded for the first time. The species also exhibited variation in the monoploid genome size, corresponding to the types of habitats occupied (grassland diploid populations had larger genome sizes than relict and subalpine diploid populations). Disregarding relict populations, the distribution of 2x and 4x cytotypes was largely parapatric, with a diffuse secondary contact zone running along the north-west margin of the Pannonian basin. Spatial segregation of the cytotypes was also observed on regional and microgeographic scales. The newly detected sympatric growth of diploids and tetraploids in isolated relict habitats most likely represents the primary zone of cytotype contact. Ploidy level was found to be a major determinant of the strength of inter-cytotype reproductive barriers. While mixed 2x + 4x populations virtually lacked the intermediate

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

PubMed Central

Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

2016-01-01

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

PubMed

Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

2016-01-01

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

Phylogenetic and microsatellite markers for Tulasnella (Tulasnellaceae) mycorrhizal fungi associated with Australian orchids.

PubMed

Ruibal, Monica P; Peakall, Rod; Smith, Leon M; Linde, Celeste C

2013-03-01

Phylogenetic and microsatellite markers were developed for Tulasnella mycorrhizal fungi to investigate fungal species identity and diversity. These markers will be useful in future studies investigating the phylogenetic relationship of the fungal symbionts, specificity of orchid-mycorrhizal associations, and the role of mycorrhizae in orchid speciation within several orchid genera. • We generated partial genome sequences of two Tulasnella symbionts originating from Chiloglottis and Drakaea orchid species with 454 genome sequencing. Cross-genus transferability across mycorrhizal symbionts associated with multiple genera of Australian orchids (Arthrochilus, Chiloglottis, Drakaea, and Paracaleana) was found for seven phylogenetic loci. Five loci showed cross-transferability to Tulasnella from other orchid genera, and two to Sebacina. Furthermore, 11 polymorphic microsatellite loci were developed for Tulasnella from Chiloglottis. • Highly informative markers were obtained, allowing investigation of mycorrhizal diversity of Tulasnellaceae associated with a wide variety of terrestrial orchids in Australia and potentially worldwide.

Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci.

PubMed

Nardelli, Maximiliano; Ibáñez, Ezequiel Alejandro; Dobler, Dara; Justy, Fabienne; Delsuc, Frédéric; Abba, Agustín Manuel; Cassini, Marcelo Hernán; Túnez, Juan Ignacio

2016-08-01

The screaming hairy armadillo (Chaetophractus vellerosus) is a mammal species containing disjunct and isolated populations. In order to assess the effect of habitat fragmentation and geographic isolation, we developed seven new microsatellite loci isolated from low-coverage genome shotgun sequencing data for this species. Among these loci, six microsatellites were found to be polymorphic with 8-26 alleles per locus detected across 69 samples analyzed from a relictual population of the species located in the northeast of the Buenos Aires Province (Argentina). Mean allelic richness and polymorphic information content were 15 and 0.75, with observed and expected heterozygosities ranging from 0.40 to 0.67 and 0.58 to 0.90, respectively. All loci showed departures from Hardy-Weinberg equilibrium. The analysis of population structure in this relictual population revealed three groups of individuals that are genetically differentiated. These newly developed microsatellites will constitute a very useful tool for the estimation of genetic diversity and structure, population dynamics, social structure, parentage and mating system in this little-studied armadillo species. Such genetic data will be particularly helpful for the development of conservation strategies for this isolated population and also for the endangered Bolivian populations previously recognized as a distinct species (Chaetophractus nationi).

Microsatellite loci analysis for the genetic variability and the parentage test of five dog breeds in South Korea.

PubMed

Kang, Byeong-Teck; Kim, Kyung-Seok; Min, Mi-Sook; Chae, Young-Jin; Kang, Jung-Won; Yoon, Junghee; Choi, Jihye; Seong, Je-Kyung; Park, Han-Chan; An, Junghwa; Lee, Mun-Han; Park, Hee-Myung; Lee, Hang

2009-06-01

To investigate the population structure of five dog breeds in South Korea and to validate polymorphic microsatellite markers for the parentage test, microsatellite loci analyses were conducted for two Korean native dog breeds, Poongsan and Jindo, and three imported dog breeds, German Shepherd, Beagle and Greyhound. Overall genetic diversity was high across all dog breeds (expected heterozygosity range: 0.71 to 0.85), although breeds differed in deviations from Hardy-Weinberg equilibrium (HWE). Significant reduction of heterozygosity in the Poongsan and Greyhound breeds was caused by non-random mating and population substructure within these breeds (the Wahlund effects). The close relationship and high degree of genetic diversity for two Korean native dog breeds were substantial. The mean polymorphism information content value was highest in Jindos (0.82) and Poongsans (0.81), followed by Beagles (0.74), Greyhounds (0.72), and German Shepherds (0.66). Accumulated exclusion power values, as an indication of marker validity for parentage tests, were varied but very high across breeds, 0.9999 for Jindos, Poongsans, and Beagles, 0.9997 for Greyhounds, and 0.9995 for German Shepherds. Taken together, the microsatellite loci investigated in this study can serve as suitable markers for the parentage test and as individual identification to establish a reliable pedigree verification system of dog breeds in South Korea. This study also stresses that the population subdivision within breeds can become an important cause of deviation from HWE in dog breeds.

Alelle number and heterozigosity for microsatellite loci in different stingless bee species (Hymenoptera: Apidae, Meliponini).

PubMed

Francisco, Flávio de O; Brito, Rute M; Arias, Maria C

2006-01-01

In the present study we compare genetic characteristics (allele diversity and observed heterozygosity) of microsatellite loci, from three stingless bee species (Plebeia remota Holmberg, Partamona mulata Moure In Camargo and Partamona helleri Friese), amplified by using heterospecific primers originally designed for Melipona bicolor Lepeletier and Scaptotrigona postica Latreille. We analyzed 360 individuals of P. remota from 72 nests, 58 individuals of R. mulata from 58 nests, and 47 individuals of P. helleri from 47 nests. The three species studied showed low level of polymorphism for the loci amplified with primers derived from M. bicolor. However, for the loci amplified with primers derived from S. postica, only P. remota presented low level of polymorphism.

Development of genomic microsatellite multiplex PCR using dye-labeled universal primer and its validation in pedigree analysis of Pacific oyster ( Crassostrea gigas)

NASA Astrophysics Data System (ADS)

Liu, Ting; Li, Qi; Song, Junlin; Yu, Hong

2017-02-01

There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

Development of novel microsatellite markers for Holothurian scabra (Holothuriidae), Apostichopus japonicas (Stichopodidae) and cross-species testing in other sea cucumbers

NASA Astrophysics Data System (ADS)

Shangguan, Jingbo; Li, Zhongbao

2017-06-01

Thirty-five new microsatellite loci from the sea cucumbers Holothurian scabra (Jaeger, 1833) and Apostichopus japonicas (Selenka, 1867) were screened and characterized using the method of magnetic bead enrichment. Of the twenty-four polymorphic loci tested, eighteen were consistent with Hardy-Weinberg equilibrium after a modified false discovery rate (B-Y FDR) correction, whereas six showed statistically significant deviations (CHS2 and CHS11: P <0.014790; FCS1, FCS6, FCS8 and FCS14: P <0.015377). Furthermore, four species of plesiomorphous and related sea cucumbers (Holothurian scabra, Holothuria leucospilota, Stichopus horrens and Apostichopus japonicas) were tested for mutual cross-amplification using a total of ninety microsatellite loci. Although transferability and universality of all loci were generally low, the results of the cross-species study showed that the markers can be applied to identify individuals to species according to the presence or absence of specific microsatellite alleles. The microsatellite markers reported here will contribute to the study of genetic diversity, assisted breeding, and population conservation in sea cucumbers, as well as allow for the identification of individuals to closely related species.

Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

PubMed Central

Zhou, He; Ma, Tian-Yu; Zhang, Rui; Xu, Qi-Zheng; Shen, Fu; Qin, Yan-Jie; Xu, Wen; Wang, Yuan; Li, Ya-Juan

2016-01-01

In this study, we selected natural polyploidy loach (diploid, triploid and tetraploid) and hybrid F1 generation obverse cross (4 × 2) and inverse cross (2 × 4) by diploids and tetraploids as the research model. The MSAP (methylation-sensitive amplified polymorphism) reaction system was established by our laboratory to explore methylation levels and pattern diversification features at the whole genome level of the polyploidy loach. The results showed that the total methylation and full methylation rates decreased on increased ploidy individuals; moreover, the hemimethylation rate showed no consistent pattern. Compared with diploid loach, the methylation patterns of tetraploid sites changed 68.17%, and the methylation patterns of triploid sites changed 73.05%. The proportion of hypermethylation genes is significantly higher than the proportion of demethylation genes. The methylation level of reciprocal cross F1 generation is lower than the male diploid and higher than the female tetraploid. The hemimethylation and total methylation rate of the cross hybrid F1 generation is significantly higher than the orthogonal F1 generation (p < 0.01). After readjusting, the methylation pattern of genome DNA of reciprocal hybrids changed 69.59% and 72.83%, respectively. PMID:27556458

Development of pedigree classification using microsatellite and mitochondrial markers for Giant grouper broodstock (Epinephelus lanceolatus) management in Taiwan.

PubMed

Kuo, Hsiao-Che; Hsu, Hao-Hsuan; Chua, Chee Shin; Wang, Ting-Yu; Chen, Young-Mao; Chen, Tzong-Yueh

2014-04-30

Most giant groupers in the market are derived from inbred stock. Inbreeding can cause trait depression, compromising the animals' fitness and disease resistance, obligating farmers to apply increased amounts of drugs. In order to solve this problem, a pedigree classification method is needed. Here, microsatellite and mitochondrial DNA were used as genetic markers to analyze the genetic relationships among giant grouper broodstocks. The 776-bp fragment of high polymorphic mitochondrial D-loop sequence was selected for measuring sibling relatedness. In a sample of 118 giant groupers, 42 haplotypes were categorized, with nucleotide diversity (π) of 0.00773 and haplotype diversity (HD) of 0.983. Furthermore, microsatellites were used for investigation of parentage. Six out of 33 microsatellite loci were selected as markers based on having a high number of alleles and compliance with Hardy-Weinberg equilibrium. Microsatellite profiles based on these loci provide high variability with low combined non-exclusion probability, permitting practical use in aquaculture. The method described here could be used to improve grouper broodstock management and lower the chances of inbreeding. This approach is expected to lead to production of higher quality groupers with higher disease resistance, thereby reducing the need for drug application.

Development of Pedigree Classification Using Microsatellite and Mitochondrial Markers for Giant Grouper Broodstock (Epinephelus lanceolatus) Management in Taiwan

PubMed Central

Kuo, Hsiao-Che; Hsu, Hao-Hsuan; Chua, Chee Shin; Wang, Ting-Yu; Chen, Young-Mao; Chen, Tzong-Yueh

2014-01-01

Most giant groupers in the market are derived from inbred stock. Inbreeding can cause trait depression, compromising the animals’ fitness and disease resistance, obligating farmers to apply increased amounts of drugs. In order to solve this problem, a pedigree classification method is needed. Here, microsatellite and mitochondrial DNA were used as genetic markers to analyze the genetic relationships among giant grouper broodstocks. The 776-bp fragment of high polymorphic mitochondrial D-loop sequence was selected for measuring sibling relatedness. In a sample of 118 giant groupers, 42 haplotypes were categorized, with nucleotide diversity (π) of 0.00773 and haplotype diversity (HD) of 0.983. Furthermore, microsatellites were used for investigation of parentage. Six out of 33 microsatellite loci were selected as markers based on having a high number of alleles and compliance with Hardy-Weinberg equilibrium. Microsatellite profiles based on these loci provide high variability with low combined non-exclusion probability, permitting practical use in aquaculture. The method described here could be used to improve grouper broodstock management and lower the chances of inbreeding. This approach is expected to lead to production of higher quality groupers with higher disease resistance, thereby reducing the need for drug application. PMID:24796300

Microsatellite markers for the endangered Roanoke logperch, Percina rex (Percidae) and their potential utility for other darter species.

PubMed

Dutton, Daniel J; Roberts, James H; Angermeier, Paul L; Hallerman, Eric M

2008-07-01

The Roanoke logperch (Percina rex Jordan and Evermann), an endangered fish, occurs in only six watersheds in the Roanoke and Chowan river drainages of Virginia, USA. The species' population genetic structure is poorly known. We developed 16 microsatellite markers that were reliably scorable and polymorphic P. rex. Markers were also screened in seven other darter species of the genus Percina. Most markers exhibited successful amplification and polymorphism in several species. These markers may therefore prove useful for population genetic studies in other darters, a diverse but highly imperiled group. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

PubMed

Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

2015-09-25

In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

Characterization of genome-wide microsatellite markers in rabbitfishes, an important resource for artisanal fisheries in the Indo-West Pacific.

PubMed

Kiper, Ilkser Erdem; Bloomer, Paulette; Borsa, Philippe; Hoareau, Thierry Bernard

2018-02-01

Rabbitfishes are reef-associated fishes that support local fisheries throughout the Indo-West Pacific region. Sound management of the resource requires the development of molecular tools for appropriate stock delimitation of the different species in the family. Microsatellite markers were developed for the cordonnier, Siganus sutor, and their potential for cross-amplification was investigated in 12 congeneric species. A library of 792 repeat-containing sequences was built. Nineteen sets of newly developed primers, and 14 universal finfish microsatellites were tested in S. sutor. Amplification success of the 19 Siganus-specific markers ranged from 32 to 79% in the 12 other Siganus species, slightly decreasing when the genetic distance of the target species to S. sutor increased. Seventeen of these markers were polymorphic in S. sutor and were further assayed in S. luridus, S. rivulatus, and S. spinus, of which respectively 9, 10 and 8 were polymorphic. Statistical power analysis and an analysis of molecular variance showed that subtle genetic differentiation can be detected using these markers, highlighting their utility for the study of genetic diversity and population genetic structure in rabbitfishes.

Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing

PubMed Central

Fortuna, Taiadjana M.; Snirc, Alodie; Badouin, Hélène; Gouzy, Jérome; Siguenza, Sophie; Esquerre, Diane; Le Prieur, Stéphanie; Shykoff, Jacqui A.; Giraud, Tatiana

2016-01-01

Background Anther-smut fungi belonging to the genus Microbotryum sterilize their host plants by aborting ovaries and replacing pollen by fungal spores. Sibling Microbotryum species are highly specialized on their host plants and they have been widely used as models for studies of ecology and evolution of plant pathogenic fungi. However, most studies have focused, so far, on M. lychnidis-dioicae that parasitizes the white campion Silene latifolia. Microbotryum saponariae, parasitizing mainly Saponaria officinalis, is an interesting anther-smut fungus, since it belongs to a tetrapolar lineage (i.e., with two independently segregating mating-type loci), while most of the anther-smut Microbotryum fungi are bipolar (i.e., with a single mating-type locus). Saponaria officinalis is a widespread long-lived perennial plant species with multiple flowering stems, which makes its anther-smut pathogen a good model for studying phylogeography and within-host multiple infections. Principal Findings Here, based on a generated genome sequence of M. saponariae we developed 6 multiplexes with a total of 22 polymorphic microsatellite markers using an inexpensive and efficient method. We scored these markers in fungal individuals collected from 97 populations across Europe, and found that the number of their alleles ranged from 2 to 11, and their expected heterozygosity from 0.01 to 0.58. Cross-species amplification was examined using nine other Microbotryum species parasitizing hosts belonging to Silene, Dianthus and Knautia genera. All loci were successfully amplified in at least two other Microbotryum species. Significance These newly developed markers will provide insights into the population genetic structure and the occurrence of within-host multiple infections of M. saponariae. In addition, the draft genome of M. saponariae, as well as one of the described markers will be useful resources for studying the evolution of the breeding systems in the genus Microbotryum and the

Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liao, D.; Weiner, A.M.

1995-12-10

The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to studymore » the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.« less

Characterization of Mauritius parakeet (Psittacula eques) microsatellite loci and their cross-utility in other parrots (Psittacidae, Aves).

PubMed

Raisin, Claire; Dawson, Deborah A; Greenwood, Andrew G; Jones, Carl G; Groombridge, Jim J

2009-07-01

We characterized 21 polymorphic microsatellite loci in the endangered Mauritius parakeet (Psittacula eques). Loci were isolated from a Mauritius parakeet genomic library that had been enriched separately for eight different repeat motifs. Loci were characterized in up to 43 putatively unrelated Mauritius parakeets from a single population inhabiting the Black River Gorges National Park, Mauritius. Each locus displayed between three and nine alleles, with the observed heterozygosity ranging between 0.39 and 0.96. All loci were tested in 10 other parrot species. Despite testing few individuals, between seven and 21 loci were polymorphic in each of seven species tested. © 2009 Blackwell Publishing Ltd.

Eighteen microsatellite loci in Salix arbutifolia (Salicaceae) and cross-species amplification in Salix and Populus species.

PubMed

Hoshikawa, Takeshi; Kikuchi, Satoshi; Nagamitsu, Teruyoshi; Tomaru, Nobuhiro

2009-07-01

Salix arbutifolia is a riparian dioecious tree species that is of conservation concern in Japan because of its highly restricted distribution. Eighteen polymorphic loci of dinucleotide microsatellites were isolated and characterized. Among these, estimates of the expected heterozygosity ranged from 0.350 to 0.879. Cross-species amplification was successful at 9-13 loci among six Salix species and at three loci in one Populus species. © 2009 Blackwell Publishing Ltd.

High ploidy diversity and distinct patterns of cytotype distribution in a widespread species of Oxalis in the Greater Cape Floristic Region

PubMed Central

Krejčíková, Jana; Sudová, Radka; Lučanová, Magdalena; Trávníček, Pavel; Urfus, Tomáš; Vít, Petr; Weiss-Schneeweiss, Hanna; Kolano, Bożena; Oberlander, Kenneth; Dreyer, Leanne L.; Suda, Jan

2013-01-01

Background and Aims Genome duplication is widely acknowledged as a major force in the evolution of angiosperms, although the incidence of polyploidy in different floras may differ dramatically. The Greater Cape Floristic Region of southern Africa is one of the world's biodiversity hotspots and is considered depauperate in polyploids. To test this assumption, ploidy variation was assessed in a widespread member of the largest geophytic genus in the Cape flora: Oxalis obtusa. Methods DNA flow cytometry complemented by confirmatory chromosome counts was used to determine ploidy levels in 355 populations of O. obtusa (1014 individuals) across its entire distribution range. Ecological differentiation among cytotypes was tested by comparing sets of vegetation and climatic variables extracted for each locality. Key Results Three majority (2x, 4x, 6x) and three minority (3x, 5x, 8x) cytotypes were detected in situ, in addition to a heptaploid individual originating from a botanical garden. While single-cytotype populations predominate, 12 mixed-ploidy populations were also found. The overall pattern of ploidy level distribution is quite complex, but some ecological segregation was observed. Hexaploids are the most common cytotype and prevail in the Fynbos biome. In contrast, tetraploids dominate in the Succulent Karoo biome. Precipitation parameters were identified as the most important climatic variables associated with cytotype distribution. Conclusions Although it would be premature to make generalizations regarding the role of genome duplication in the genesis of hyperdiversity of the Cape flora, the substantial and unexpected ploidy diversity in Oxalis obtusa is unparalleled in comparison with any other cytologically known native Cape plant species. The results suggest that ploidy variation in the Greater Cape Floristic Region may be much greater than currently assumed, which, given the documented role of polyploidy in speciation, has direct implications for radiation

Visual selection and maintenance of the cell lines with high plant regeneration ability and low ploidy level in Dianthus acicularis by monitoring with flow cytometry analysis.

PubMed

Shiba, Tomonori; Mii, Masahiro

2005-12-01

Efficient plant regeneration system from cell suspension cultures was established in D. acicularis (2n=90) by monitoring ploidy level and visual selection of the cultures. The ploidy level of the cell cultures closely related to the shoot regeneration ability. The cell lines comprising original ploidy levels (2C+4C cells corresponding to DNA contents of G1 and G2 cells of diploid plant, respectively) showed high regeneration ability, whereas those containing the cells with 8C or higher DNA C-values showed low or no regeneration ability. The highly regenerable cell lines thus selected consisted of compact cell clumps with yellowish color and relatively moderate growth, suggesting that it is possible to select visually the highly regenerable cell lines with the original ploidy level. All the regenerated plantlets from the highly regenerable cell cultures exhibited normal phenotypes and no variations in ploidy level were observed by flow cytometry (FCM) analysis.

Isolation and characterization of microsatellite markers useful for exploring introgression among species in the diverse New Zealand cicada genus Kikihia.

PubMed

Wade, Elizabeth J; Simon, Chris

2015-01-01

The New Zealand cicada genus Kikihia Dugdale 1971 exhibits more than 20 contact zones between species pairs that vary widely in their divergence times (between 20,000 and 2 million years) in which some level of hybridization is evident. Mitochondrial phylogenies suggest some movement of genes across species boundaries. Biparentally inherited and quickly evolving molecular markers like microsatellites are useful for assessing gene flow levels. Here, we present six polymorphic microsatellite loci that amplify DNA from seven species across the genus Kikihia; Kikihia "northwestlandica," Kikihia "southwestlandica," Kikihia muta, Kikihia angusta, Kikihia "tuta," Kikihia "nelsonensis," and Kikihia "murihikua." The markers were developed using whole-genome shotgun sequencing on the 454 pyrosequencing platform. Moderate to high levels of polymorphisms were observed with 14-47 alleles for 213 individuals from 15 populations. Observed and expected heterozygosity range from 0 to 1 and 0.129 to 0.945, respectively. These new markers will be instrumental for the assessment of gene flow across multiple contact zones in Kikihia. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

Relook TURBT in superficial bladder cancer: its importance and its correlation with the tumor ploidy.

PubMed

Dwivedi, Udai S; Kumar, Abhay; Das, Suren K; Trivedi, Sameer; Kumar, Mohan; Sunder, Shyam; Singh, Pratap B

2009-01-01

To evaluate various prognostic factor predictors of residual growth in Relook transurethral resection of bladder tumor (TURBT) in superficial bladder cancer. Also, to evaluate the role of Relook TURBT along with the ploidy for prediction of recurrence and stage progression in these patients. Fifty patients with superficial bladder cancer underwent TURBT after complete evaluation. Ploidy of the tumor specimen was evaluated by flow cytometry. After 4 to 6 weeks of initial TURBT, these patients underwent Relook TURBT. Final treatment was given after the results of the histological evaluation of these specimens. Patients who underwent bladder sparing treatment were followed-up. Of the patients, 28.5% had residual tumor in Relook TURBT. Growth was found to be at the same site in 66.7% and at a different site 33.3%; 75% had single while 25% had multiple residual growth. Residual malignant tissue had a statistically significant correlation with size of the tumor (>3 cm), appearance (solid tumor), number (>3), grade (high), and multiple previous resections. Overall, the up-migration of stage and grade leads to change in treatment in 41.6%; 5 underwent radical cystectomy and 1 opted for radiotherapy; in 2 patients, intravesical BCG was given. In follow-up of mean 11.5 months, 16.6% had recurrence. Presence of residual growth in Relook TURBT along with number, size, morphology, and multiple previous resections were found to have significant correlation with the recurrence in these patients. Ploidy and grade of the tumor were not found to have correlation. Multiple, more than 3 cm, solid high grade tumor with > 3 previous resections were predictors of presence of residual tumor in Relook TURBT. Presence of residual growth is a significant risk factor for recurrence. Ploidy was not found to be significantly correlated with recurrence.

Comparison of microsatellite variations between Red Junglefowl and a commercial chicken gene pool.

PubMed

Tadano, R; Kinoshita, K; Mizutani, M; Tsudzuki, M

2014-02-01

It is assumed that Red Junglefowl (Gallus gallus) is one of the main ancestors of domestic chickens (Gallus gallus domesticus). Differences in microsatellite polymorphisms between Red Junglefowl and modern commercial chickens, which are used for egg and meat production, have not been fully reported. A total of 361 individuals from 1 Red Junglefowl population that has been maintained as a closed flock, 5 final cross-bred commercial layer populations (white-, tinted-, and brown-egg layers), and 2 final cross-bred commercial broiler populations were genotyped for 40 autosomal microsatellite loci. We compared microsatellite variations in Red Junglefowl with those in a commercial chicken gene pool. The contribution of each population to the genetic diversity was also estimated based on the molecular coancestry. In total, 302 distinct alleles were detected in 1 Red Junglefowl and 7 commercial chicken populations, of which 31 alleles (10.3%) were unique to Red Junglefowl, most of which occurred at a high frequency. The genetic differentiation between Red Junglefowl and commercial chickens (pairwise FST) ranged from 0.32 to 0.47. According to the neighbor-joining tree based on the modified Cavalli-Sforza chord distances and the Bayesian clustering analysis, Red Junglefowl was genetically distant from the commercial chicken gene pool tested. In all of the populations analyzed, Red Junglefowl made the highest contribution to genetic diversity. These results suggest that Red Junglefowl has a distinct distribution of microsatellite alleles and that there is a high level of genetic divergence between Red Junglefowl and commercial chickens.

avpr1a length polymorphism is not associated with either social or genetic monogamy in free-living prairie voles.

PubMed

Mabry, Karen E; Streatfeild, Craig A; Keane, Brian; Solomon, Nancy G

2011-01-01

Recent discoveries of single-gene influences on social behaviour have generated a great deal of interest in the proximate mechanisms underlying the expression of complex behaviours. Length polymorphism in a microsatellite in the regulatory region of the gene encoding the vasopressin 1a receptor (avpr1a) has been associated with both inter- and intra-specific variation in socially monogamous behaviour in voles (genus Microtus) under laboratory conditions. Here, we evaluate the relationship between avpr1a length polymorphism and social associations, genetic monogamy, and reproductive success in free-living prairie vole (M. ochrogaster) populations. We found no evidence of a relationship between avpr1a microsatellite length and any of our correlates of either social or genetic monogamy in the field. Our results, especially when taken in conjunction with those of recent experimental studies in semi-natural enclosures, suggest that avpr1a polymorphism is unlikely to have been a major influence in the evolution or maintenance of social monogamy in prairie voles under natural conditions.

Development of microsatellite markers in Myotis sodalis and cross-species amplification in M. gricescens, M. leibii, M. lucifugus, and M. septentrionalis

Treesearch

Robert G. Trujillo; Sybill K. Amelon

2009-01-01

The Indiana bat (Myotis sodalis) is a highly endangered vespertilionid bat whose distribution is associated with limestone caves in the eastern United States. We present nine new polymorphic nuclear microsatellite markers for Myotis sodalis developed using an enriched library method. A total of 62 M. sodalis...

Efficiency of semi-automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations.

PubMed

Bonnet, A; Thévenon, S; Maudet, F; Maillard, J C

2002-10-01

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.

Investigating the genetic diversity of Echinococcus granulosus sensu stricto with new microsatellites.

PubMed

Umhang, Gérald; Grenouillet, Frédéric; Bastid, Vanessa; M'Rad, Selim; Valot, Benoît; Oudni-M'Rad, Myriam; Babba, Hamouda; Boué, Franck

2018-06-18

Cystic echinococcosis is a zoonotic disease with worldwide distribution caused by the larval stage of the Cestode parasite Echinococcus granulosus sensu lato. Due to the predominance or even the exclusive presence of E. granulosus sensu stricto (s.s.) among E. granulosus species in many areas, the genetic diversity needs to be further investigated at the species level to better understand the inter- and intra-focus epidemiological features. Short sequences of mitochondrial or nuclear genes generally lack or have limited discriminatory power, hindering the detection of polymorphisms to reflect geographically based peculiarities and/or any history of infection. A high discriminatory power can only be reached by sequencing complete or near complete mitogenomes or relatively long nuclear sequences, which is time-consuming and onerous. To overcome this issue, a systematic research for single-locus microsatellites was performed on the nuclear genome of E. granulosus s.s. in order to investigate its intra-species genetic diversity. Two microsatellites, EgSca6 and EgSca11, were selected and characterized. The test of a panel of 75 cystic echinococcosis samples revealed a very high discrimination index of 0.824 for EgSca6, 0.987 for EgSca11, and 0.994 when multiplexing both microsatellites. Testing cystic echinococcosis samples from both liver and lungs in five sheep revealed that these two microsatellites appear to be of particular interest for investigating genetic diversity at the intra-individual host level. As this method has many advantages compared to classical sequencing, the availability of other targets means that it is potentially possible to constitute a panel facilitating large-scale molecular epidemiology studies for E. granulosus s.l.

Genome-Wide Development and Use of Microsatellite Markers for Large-Scale Genotyping Applications in Foxtail Millet [Setaria italica (L.)

PubMed Central

Pandey, Garima; Misra, Gopal; Kumari, Kajal; Gupta, Sarika; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

2013-01-01

The availability of well-validated informative co-dominant microsatellite markers and saturated genetic linkage map has been limited in foxtail millet (Setaria italica L.). In view of this, we conducted a genome-wide analysis and identified 28 342 microsatellite repeat-motifs spanning 405.3 Mb of foxtail millet genome. The trinucleotide repeats (∼48%) was prevalent when compared with dinucleotide repeats (∼46%). Of the 28 342 microsatellites, 21 294 (∼75%) primer pairs were successfully designed, and a total of 15 573 markers were physically mapped on 9 chromosomes of foxtail millet. About 159 markers were validated successfully in 8 accessions of Setaria sp. with ∼67% polymorphic potential. The high percentage (89.3%) of cross-genera transferability across millet and non-millet species with higher transferability percentage in bioenergy grasses (∼79%, Switchgrass and ∼93%, Pearl millet) signifies their importance in studying the bioenergy grasses. In silico comparative mapping of 15 573 foxtail millet microsatellite markers against the mapping data of sorghum (16.9%), maize (14.5%) and rice (6.4%) indicated syntenic relationships among the chromosomes of foxtail millet and target species. The results, thus, demonstrate the immense applicability of developed microsatellite markers in germplasm characterization, phylogenetics, construction of genetic linkage map for gene/quantitative trait loci discovery, comparative mapping in foxtail millet, including other millets and bioenergy grass species. PMID:23382459

Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)].

PubMed

Pandey, Garima; Misra, Gopal; Kumari, Kajal; Gupta, Sarika; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj

2013-04-01

The availability of well-validated informative co-dominant microsatellite markers and saturated genetic linkage map has been limited in foxtail millet (Setaria italica L.). In view of this, we conducted a genome-wide analysis and identified 28 342 microsatellite repeat-motifs spanning 405.3 Mb of foxtail millet genome. The trinucleotide repeats (∼48%) was prevalent when compared with dinucleotide repeats (∼46%). Of the 28 342 microsatellites, 21 294 (∼75%) primer pairs were successfully designed, and a total of 15 573 markers were physically mapped on 9 chromosomes of foxtail millet. About 159 markers were validated successfully in 8 accessions of Setaria sp. with ∼67% polymorphic potential. The high percentage (89.3%) of cross-genera transferability across millet and non-millet species with higher transferability percentage in bioenergy grasses (∼79%, Switchgrass and ∼93%, Pearl millet) signifies their importance in studying the bioenergy grasses. In silico comparative mapping of 15 573 foxtail millet microsatellite markers against the mapping data of sorghum (16.9%), maize (14.5%) and rice (6.4%) indicated syntenic relationships among the chromosomes of foxtail millet and target species. The results, thus, demonstrate the immense applicability of developed microsatellite markers in germplasm characterization, phylogenetics, construction of genetic linkage map for gene/quantitative trait loci discovery, comparative mapping in foxtail millet, including other millets and bioenergy grass species.

Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences1

PubMed Central

Gardner, Elliot M.; Laricchia, Kristen M.; Murphy, Matthew; Ragone, Diane; Scheffler, Brian E.; Simpson, Sheron; Williams, Evelyn W.; Zerega, Nyree J. C.

2015-01-01

Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. Conclusions: These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit. PMID:26421253

Isolation and Characterization of Microsatellite Loci for Hibiscus aridicola (Malvaceae), an Endangered Plant Endemic to the Dry-Hot Valleys of Jinsha River in Southwest China

PubMed Central

Zhang, Le; Sun, Weibang; Wang, Zhonglang; Guan, Kaiyun; Yang, Junbo

2011-01-01

Hibiscus aridicola (Malvaceae) is an endangered ornamental shrub endemic to the dry-hot valleys of Jinsha River in southwest China. Only four natural populations of H. aridicola exist in the wild according to our field investigation. It can be inferred that H. aridicola is facing a very high risk of extinction in the wild and an urgent conservation strategy is required. By using a modified biotin-streptavidin capture method, a total of 40 microsatellite markers were developed and characterized in H. aridicola for the first time. Polymorphisms were evaluated in 39 individuals from four natural populations. Fifteen of the markers showed polymorphisms with two to six alleles per locus; the observed heterozygosity ranged from 0.19 to 0.72. These microsatellite loci would be useful tools for population genetics studies on H. aridicola and other con-generic species which are important to the conservation and development of endangered species. PMID:22016620

Anatomic Site Based Ploidy Analysis of Oral Premalignant Lesions

PubMed Central

Islam, M. N.; Kornberg, L.; Veenker, E.; Cohen, D. M.

2009-01-01

The location of oral leukoplakia correlates strongly with the probability of finding dysplastic or malignant alterations at biopsy. It is well established that early detection can dramatically improve the 5-year survival rates for oral squamous cell carcinomas. Since aneuploidy is predictive of future conversion to malignancy, we hypothesized that dysplastic lesions from high-risk sites (floor of mouth, tongue and lips) would exhibit greater aneuploidy than low-risk sites (palate, gingiva and buccal mucosa). Epithelial sections from 60 archival samples diagnosed as mild dysplasia (36 females, 20 males) from various high/low risk locations were stained with Blue Feulgen Stain for DNA Ploidy Analysis (Clarient, Aliso Viejo, CA) and ploidy was analyzed using a ChromaVision ACIS II (Clarient, ALiso Viejo, CA) Image cytometry system. A DNA histogram was generated using an image analyzing software that evaluated the amount of Feulgen stain which is proportional to the amount of nuclear DNA. An ANOVA analysis followed by the Student’s‘t’ test revealed significant differences between means (P ≤ 0.05). Lesions originating from lateral/ventral tongue (85%), floor of mouth (50%) and soft palate (44%) exhibited a higher frequency of aneuploidy than lesions from gingiva (22%) and lower lip (25%). This pilot study demonstrates that dysplastic lesions from high-risk sites such as the floor of the mouth and lateral/ventral tongue have higher frequency of aneuploidy. PMID:20237983

Molecular diversity of Pakistani mango (Mangifera indica L.) varieties based on microsatellite markers.

PubMed

Nazish, T; Shabbir, G; Ali, A; Sami-Ul-Allah, S; Naeem, M; Javed, M; Batool, S; Arshad, H; Hussain, S B; Aslam, K; Seher, R; Tahir, M; Baber, M

2017-04-05

Understanding the genetic diversity of different Pakistani mango varieties is important for germplasm management and varietal characterization. Microsatellites are efficient and highly polymorphic markers for comparative genome mapping, and were used in the present study to determine the genetic relatedness and variability among 15 indigenous mango cultivars (Mangifera indica L.). Overall, 181 bands were produced using 12 simple sequence repeat (SSR) primers. Out of the 12 primers used, 10 were polymorphic and two were monomorphic. Genetic relatedness among cultivars was assessed by constructing a dendrogram using the unweighted pair group method of arithmetic means. The accessions exhibited coefficients of similarity ranging from 75 to 100%, indicating the frequent use of only a few parent cultivars and the presence of inbreeding. The primers used in the present study were found to be valuable for identifying genetic relationships among mango cultivars.

Novel microsatellites for Calibrachoa heterophylla (Solanaceae) endemic to the South Atlantic Coastal Plain of South America1

PubMed Central

Silva-Arias, Gustavo Adolfo; Mäder, Geraldo; Bonatto, Sandro L.; Freitas, Loreta B.

2015-01-01

Premise of the study: Calibrachoa heterophylla (Solanaceae) is a petunia species restricted to the South Atlantic Coastal Plain of South America and presents a recent history of colonization from continental to coastal environments and diversification following the formation of the Coastal Plain during the Quaternary period. Methods and Results: This study reports a suite of 16 microsatellite loci for C. heterophylla. The applicability of these markers was assessed by genotyping 57 individuals from two natural populations. Of the 16 described loci, 12 were found to be polymorphic. Successful cross-amplification tests were obtained using 12 Calibrachoa species. Conclusions: The development of microsatellite markers will be useful to recover the contemporary history of the colonization of the Coastal Plain and to provide information for the conservation of this endemic species. PMID:26191462

Major histocompatibility complex class I chain related gene-A microsatellite polymorphism shows secondary association with type 1 diabetes and celiac disease in North Indians.

PubMed

Kumar, N; Sharma, G; Kaur, G; Tandon, N; Bhatnagar, S; Mehra, N

2012-10-01

Microsatellite polymorphism in exon 5 of major histocompatibility complex class I chain related gene-A (MIC-A) has been implicated in the etiology of autoimmune diseases including type 1 diabetes (T1D) and celiac disease (CD). In this study on North Indian population, the MIC-A5.1 allele, carrying a premature termination codon in transmembrane region, was observed with increased frequency in T1D (29.6%, odds ratio OR = 2.1, P = 0.00017) and CD patients (40.3%, OR = 3.37, P = 1.67E-05) than in controls (16.7%). When the MIC-A5.1 association was adjusted for linkage with human leukocyte antigen (HLA)-DR3, the statistical significance of the association was abolished. This implies that the observed association of MIC-A5.1 is due to its linkage disequilibrium (D' = 0.94) with HLA-B8-DR3-DQ2 haplotype and is secondary to the overall association with DR3 positive MHC haplotypes. © 2012 John Wiley & Sons A/S.

Development of novel microsatellite markers for Holothurian scabra (Holothuriidae), Apostichopus japonicas (Stichopodidae) and cross-species testing in other sea cucumbers

NASA Astrophysics Data System (ADS)

Shangguan, Jingbo; Li, Zhongbao

2018-03-01

Thirty-five new microsatellite loci from the sea cucumbers Holothurian scabra (Jaeger, 1833) and Apostichopus japonicas (Selenka, 1867) were screened and characterized using the method of magnetic bead enrichment. Of the twenty-four polymorphic loci tested, eighteen were consistent with Hardy-Weinberg equilibrium after a modified false discovery rate (B-Y FDR) correction, whereas six showed statistically significant deviations (CHS2 and CHS11: P<0.014 790; FCS1, FCS6, FCS8 and FCS14: P<0.015 377). Furthermore, four species of plesiomorphous and related sea cucumbers ( Holothurian scabra, Holothuria leucospilota, Stichopus horrens and Apostichopus japonicas) were tested for mutual cross-amplification using a total of ninety microsatellite loci. Although transferability and universality of all loci were generally low, the results of the cross-species study showed that the markers can be applied to identify individuals to species according to the presence or absence of specific microsatellite alleles. The microsatellite markers reported here will contribute to the study of genetic diversity, assisted breeding, and population conservation in sea cucumbers, as well as allow for the identification of individuals to closely related species.

Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

PubMed Central

Boutte, Julien; Aliaga, Benoît; Lima, Oscar; Ferreira de Carvalho, Julie; Ainouche, Abdelkader; Macas, Jiri; Rousseau-Gueutin, Mathieu; Coriton, Olivier; Ainouche, Malika; Salmon, Armel

2015-01-01

Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. PMID:26530424

Characterization of microsatellite loci in the Himalayan lichen fungus Lobaria pindarensis (Lobariaceae).

PubMed

Devkota, Shiva; Cornejo, Carolina; Werth, Silke; Chaudhary, Ram Prasad; Scheidegger, Christoph

2014-05-01

Microsatellite loci were developed for the rare, Himalayan, endemic haploid lichen fungus, Lobaria pindarensis, to study its population subdivision and the species' response to forest disturbance and fragmentation. • We developed 18 polymorphic microsatellite markers using 454 pyrosequencing data and assessed them in 109 individuals. The number of alleles per locus ranged from three to 11 with an average of 6.9. Nei's unbiased gene diversity, averaged over loci, ranged from 0.514 to 0.685 in the three populations studied. The cross-amplification success with related species (L. chinensis, L. gyrophorica, L. isidiophora, L. orientalis, L. pulmonaria, L. spathulata, and Lobaria sp.) was generally high and decreased with decreasing relationship to L. pindarensis. • The new markers will allow the study of genetic diversity and differentiation within L. pindarensis across its distribution. Moreover, they will enable us to study the effects of forest management on the genetic population structure of this tree-colonizing lichen and to carry out population genetic studies of related species in East Asia.

Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

NASA Astrophysics Data System (ADS)

Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

2014-08-01

Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae).

PubMed

Barth, Susanne; Jankowska, Marta Jolanta; Hodkinson, Trevor Roland; Vellani, Tia; Klaas, Manfred

2016-03-22

Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3% Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands.

Development and validation of 697 novel polymorphic genomic and EST-SSR markers in the American cranberry (Vaccinium macrocarpon Ait.).

PubMed

Schlautman, Brandon; Fajardo, Diego; Bougie, Tierney; Wiesman, Eric; Polashock, James; Vorsa, Nicholi; Steffan, Shawn; Zalapa, Juan

2015-01-27

The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level, and contained moderate to high levels of polymorphism with a polymorphic information content >0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.

Epigenetic contribution to successful polyploidizations: variation in global cytosine methylation along an extensive ploidy series in Dianthus broteri (Caryophyllaceae).

PubMed

Alonso, Conchita; Balao, Francisco; Bazaga, Pilar; Pérez, Ricardo

2016-11-01

Polyploidization is a significant evolutionary force in plants which involves major genomic and genetic changes, frequently regulated by epigenetic factors. We explored whether natural polyploidization in Dianthus broteri complex resulted in substantial changes in global DNA cytosine methylation associated to ploidy. Global cytosine methylation was estimated by high-performance liquid chromatography (HPLC) in 12 monocytotypic populations with different ploidies (2×, 4×, 6×, 12×) broadly distributed within D. broteri distribution range. The effects of ploidy level and local variation on methylation were assessed by generalized linear mixed models (GLMMs). Dianthus broteri exhibited a higher methylation percent (˜33%) than expected by its monoploid genome size and a large variation among study populations (range: 29.3-35.3%). Global methylation tended to increase with ploidy but did not significantly differ across levels due to increased variation within the highest-order polyploidy categories. Methylation varied more among hexaploid and dodecaploid populations, despite such cytotypes showing more restricted geographic location and increased genetic relatedness than diploids and tetraploids. In this study, we demonstrate the usefulness of an HPLC method in providing precise and genome reference-free global measure of DNA cytosine methylation, suitable to advance current knowledge of the roles of this epigenetic mechanism in polyploidization processes. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis

PubMed Central

Variath, Murali Tottekkad; Joshi, Gopal; Bali, Sapinder; Agarwal, Manu; Kumar, Amar; Jagannath, Arun; Goel, Shailendra

2015-01-01

Background Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing. Principal Findings Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to

Isolation and characterization of microsatellite loci in the intertidal sponge Halichondria panicea

USGS Publications Warehouse

Knowlton, Anne L.; Pierson, Barbara J.; Talbot, S.L.; Highsmith, Ray C.

2003-01-01

GA- and CA-enriched genomic libraries were constructed for the intertidal sponge Halichondria panicea. Unique repeat motifs identified varied from the expected simple dinucleotide repeats to more complex repeat units. All sequences tended to be highly repetitive but did not necessarily contain the targeted motifs. Seven microsatellite loci were evaluated on sponges from the clone source population. All seven were polymorphic with 5.43 ± 0.92 mean number of alleles. Six of the seven loci that could be resolved had mean heterozygosities of 0.14–0.68. The loci identified here will be useful for population studies.

Phylogenetic and microsatellite markers for Tulasnella (Tulasnellaceae) mycorrhizal fungi associated with Australian orchids1

PubMed Central

Ruibal, Monica P.; Peakall, Rod; Smith, Leon M.; Linde, Celeste C.

2013-01-01

• Premise of the study: Phylogenetic and microsatellite markers were developed for Tulasnella mycorrhizal fungi to investigate fungal species identity and diversity. These markers will be useful in future studies investigating the phylogenetic relationship of the fungal symbionts, specificity of orchid–mycorrhizal associations, and the role of mycorrhizae in orchid speciation within several orchid genera. • Methods and Results: We generated partial genome sequences of two Tulasnella symbionts originating from Chiloglottis and Drakaea orchid species with 454 genome sequencing. Cross-genus transferability across mycorrhizal symbionts associated with multiple genera of Australian orchids (Arthrochilus, Chiloglottis, Drakaea, and Paracaleana) was found for seven phylogenetic loci. Five loci showed cross-transferability to Tulasnella from other orchid genera, and two to Sebacina. Furthermore, 11 polymorphic microsatellite loci were developed for Tulasnella from Chiloglottis. • Conclusions: Highly informative markers were obtained, allowing investigation of mycorrhizal diversity of Tulasnellaceae associated with a wide variety of terrestrial orchids in Australia and potentially worldwide. PMID:25202528

Development of EST-derived microsatellite markers in the aquatic macrophyte Ranunculus bungei (Ranunculaceae)1

PubMed Central

Wu, Zhigang; Wu, Jinwei; Wang, Yalin; Hou, Hongwei

2017-01-01

Premise of the study: Microsatellite or simple sequence repeat (SSR) markers were developed to investigate the influence of ecological factors on gene flow and spatial genetic structuring of the submerged plant Ranunculus bungei (Ranunculaceae), which is regarded as an important species for understanding how plants adapt to an aquatic environment. Methods and Results: Twenty-two microsatellite loci were identified from an expressed sequence tag (EST) library. The number of alleles per locus ranged from one to five, and the expected heterozygosity varied from 0.0 to 0.5 in four Chinese populations of R. bungei. Fourteen loci were polymorphic and significantly deviated from Hardy–Weinberg equilibrium. All of the loci were found to be amplifiable in two other species of Ranunculus section Batrachium, and cross-amplification in six riparian and aquatic species of Ranunculaceae was also partially successful. Conclusions: These novel EST-SSR markers will be useful for ecological and evolutionary studies of R. bungei as well as related species. PMID:28791205

Association of vWA and TPOX Polymorphisms with Venous Thrombosis in Mexican Mestizos

PubMed Central

Meraz-Ríos, Marco Antonio; Majluf-Cruz, Abraham; Santana, Carla; Noris, Gino; Camacho-Mejorado, Rafael; Acosta-Saavedra, Leonor C.; Calderón-Aranda, Emma S.; Hernández-Juárez, Jesús; Magaña, Jonathan J.; Gómez, Rocío

2014-01-01

Objective. Venous thromboembolism (VTE) is a multifactorial disorder and, worldwide, the most important cause of morbidity and mortality. Genetic factors play a critical role in its aetiology. Microsatellites are the most important source of human genetic variation having more phenotypic effect than many single nucleotide polymorphisms. Hence, we evaluate a possible relationship between VTE and the genetic variants in von Willebrand factor, human alpha fibrinogen, and human thyroid peroxidase microsatellites to identify possible diagnostic markers. Methods. Genotypes were obtained from 177 patients with VTE and 531 nonrelated individuals using validated genotyping methods. The allelic frequencies were compared; Bayesian methods were used to correct population stratification to avoid spurious associations. Results. The vWA-18, TPOX-9, and TPOX-12 alleles were significantly associated with VTE. Moreover, subjects bearing the combination vWA-18/TPOX-12 loci exhibited doubled risk for VTE (95% CI = 1.02–3.64), whereas the combination vWA-18/TPOX-9 showed an OR = 10 (95% CI = 4.93–21.49). Conclusions. The vWA and TPOX microsatellites are good candidate biomarkers in venous thromboembolism diseases and could help to elucidate their origins. Additionally, these polymorphisms could become useful markers for genetic studies of VTE in the Mexican population; however, further studies should be done owing that this data only show preliminary evidence. PMID:25250329

Microsatellites for Lindera species

Treesearch

Craig S. Echt; D. Deemer; T.L. Kubisiak; C.D. Nelson

2006-01-01

Microsatellite markers were developed for conservation genetic studies of Lindera melissifolia (pondberry), a federally endangered shrub of southern bottomland ecosystems. Microsatellite sequences were obtained from DNA libraries that were enriched for the (AC)n simple sequence repeat motif. From 35 clone sequences, 20 primer...

Evaluation of a rapid single multiplex microsatellite-based assay for use in forensic genetic investigations in dogs.

PubMed

Clark, Leigh Anne; Famula, Thomas R; Murphy, Keith E

2004-10-01

To develop a set of microsatellite markers, composed of a minimal number of these markers, suitable for use in forensic genetic investigations in dogs. Blood, tissue, or buccal epithelial cells from 364 dogs of 85 breeds and mixed breeds and 19 animals from related species in the family Canidae. 61 tetranucleotide microsatellite markers were characterized on the basis of number and size of alleles, ease of genotyping, chromosomal location, and ability to be coamplified. The range in allele size, number of alleles, total heterozygosity, and fixation index for each marker were determined by use of genotype data from 383 dogs and related species. Polymorphism information content was calculated for several breeds of dogs. 7 microsatellite markers could be coamplified. These markers were labeled with fluorescent dyes, multiplexed into a single reaction, and optimized for resolution in a commercial genetic analyzer. The multiplex set was used to identify sires for 2 mixed litters. The test was not species specific; genotype information collected for wolves, coyotes, jackals, New Guinea singing dogs, and an African wild dog could not distinguish between these species. This set of 7 microsatellite markers is useful in forensic applications (ie, identification of dogs and determination of parentage) in closely related animals and is applicable to a wide range of species belonging to the family Canidae.

Development of microsatellite markers from loquat, Eriobotrya japonica (Thunb.) Lindl.

PubMed

Gisbert, A D; Lopez-Capuz, I; Soriano, J M; Llacer, G; Romero, C; Badenes, M L

2009-05-01

Loquat (Eriobotrya japonica) is a minor fruit which has become an interesting alternative into the European fruit industry. This interest resulted in a loquat germplasm collection established at the Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain. Currently, it is the main reservoir of this species outside Asia. We developed and characterized the first 21 polymorphic microsatellite loci from a CT/AG-enriched loquat genomic library. The observed heterozygosity ranged between 0.20 and 1.00, expected heterozygosity ranged between 0.17 and 0.81, three markers were multilocus and eight loci departed significantly from Hardy-Weinberg equilibrium. These markers will facilitate diversity and genetic studies into the species. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Microsatellite loci for the stingless bee Melipona rufiventris (Hymenoptera: Apidae).

PubMed

Lopes, Denilce Meneses; D Silva, Filipe Oliveira; Fernandes Salomão, Tânia Maria; Campos, Lúcio Antônio D Oliveira; Tavares, Mara Garcia

2009-05-01

Eight microsatellite primers were developed from ISSR (intersimple sequence repeats) markers for the stingless bee Melipona rufiventris. These primers were tested in 20 M. rufiventris workers, representing a single population from Minas Gerais state. The number of alleles per locus ranged from 2 to 5 (mean = 2.63) and the observed and expected heterozygosity values ranged from 0.00 to 0.44 (mean = 0.20) and from 0.05 to 0.68 (mean = 0.31), respectively. Several loci were also polymorphic in M. quadrifasciata, M. bicolor, M. mandacaia and Partamona helleri and should prove useful in population studies of other stingless bees. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

Genetic Fingerprinting Using Microsatellite Markers in a Multiplex PCR Reaction: A Compilation of Methodological Approaches from Primer Design to Detection Systems.

PubMed

Krüger, Jacqueline; Schleinitz, Dorit

2017-01-01

Microsatellites are polymorphic DNA loci comprising repeated sequence motifs of two to five base pairs which are dispersed throughout the genome. Genotyping of microsatellites is a widely accepted tool for diagnostic and research purposes such as forensic investigations and parentage testing, but also in clinics (e.g. monitoring of bone marrow transplantation), as well as for the agriculture and food industries. The co-amplification of several short tandem repeat (STR) systems in a multiplex reaction with simultaneous detection helps to obtain more information from a DNA sample where its availability may be limited. Here, we introduce and describe this commonly used genotyping technique, providing an overview on available resources on STRs, multiplex design, and analysis.

cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications1

PubMed Central

Wani, Gowher A.; Shah, Manzoor A.; Reshi, Zafar A.; Atangana, Alain R.; Khasa, Damase P.

2014-01-01

• Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation. PMID:25202636

A suite of microsatellite markers for genetic management of captive cracids (Aves, Galliformes).

PubMed

Costa, M C; Camargo, C; Laganaro, N M; Oliveira, P R R; Davanço, P V; Azeredo, R M A; Simpson, J G P; Silveira, L F; Francisco, M R

2014-11-27

Cracids are medium to large frugivorous birds that are endemic to the Neotropics. Because of deforestation and overhunting, many species are threatened. The conservation of several species has relied on captive breeding and reintroduction in the wild, but captive populations may be inbred. Microsatellite tools can permit the construction of genetic pedigrees to reduce inbreeding, but only a few loci are available for this group of birds. Here, we present 10 novel polymorphic microsatellite loci and the cross-amplification of these and of 10 additional loci available in the literature in a panel of 5 cracid species, including 3 species with high conservation concern. We provide the first polymorphic loci for the jacutinga, Aburria jacutinga (N = 8), and red-billed curassow, Crax blumenbachii (N = 9), and additional loci for bare-faced curassow, C. fasciolata (N = 8), Alagoas curassow, Pauxi mitu (N = 5), and razor-billed curassow, P. tuberosa (N = 5). The average number of alleles was 2.9 for A. jacutinga, 2.7 for C. blumenbachii, 3.5 for C. fasciolata, 2.6 for P. mitu, and 5.7 for P. tuberosa. The mean expected heterozygosities were 0.42, 0.40, 0.48, 0.37, and 0.59, respectively. The average probabilities that the set of loci would not exclude a pair of parents of an arbitrary offspring were 2.9% in A. jacutinga, 1% in C. blumenbachii, 0.5% in C. fasciolata, 0.4% in P. mitu, and 0.002% in P. tuberosa suggesting that these loci may be adequate for parentage analysis and to implement ex situ genetic management plans.

Relationship between DNA ploidy level and tumor sociology behavior in 12 nervous cell lines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kiss, R.; Camby, I.; Salmon, I.

1995-06-01

Cell population sociology was studied in two medulloblastomas and 10 astrocytic human tumor cell lines by means of the characterization of the structure of neoplastic cell colonies growing on histological slides. This was carried out via digital cell image analysis of Feulgen-stained nuclei, to which the Delaunay triangulation and Voronoi paving mathematical techniques were applied. Such assessments were compared to the DNA ploidy level (assessed by means of DNA histogram typing). The results show that the cell colony architecture characteristics differed markedly according to whether the cell lines were euploid (diploid or tetraploid) or aneuploid (hyperdiploid, triploid, hypertriploid, or polymorphic).more » In fact, the cell colonies from the euploid cell nuclei populations were larger and more dense than those from the aneuploid ones. Furthermore, for an identical period of culture, the cell lines from high-grade malignant astrocytic tumors (glioblastomas) exhibited cell colonies that were larger and more dense than those in cell lines from low-grade astrocytic tumors (astrocytomas). In each of these two groups, the diploid cell nuclei populations exhibited cell colonies larger and more dense than the nondiploid colonies. The present methodology is now being applied in vivo to histological sections of surgically removed human brain tumors in order to distinguish between high-risk clinical subgroups and medium-risk subgroups in clearly circumscribed histopathological groups. 38 refs., 5 figs., 2 tabs.« less

avpr1a length polymorphism is not associated with either social or genetic monogamy in free-living prairie voles

PubMed Central

Mabry, Karen E.; Streatfeild, Craig A.; Keane, Brian; Solomon, Nancy G.

2010-01-01

Recent discoveries of single-gene influences on social behaviour have generated a great deal of interest in the proximate mechanisms underlying the expression of complex behaviours. Length polymorphism in a microsatellite in the regulatory region of the gene encoding the vasopressin 1a receptor (avpr1a) has been associated with both inter- and intra-specific variation in socially monogamous behaviour in voles (genus Microtus) under laboratory conditions. Here, we evaluate the relationship between avpr1a length polymorphism and social associations, genetic monogamy, and reproductive success in free-living prairie vole (M. ochrogaster) populations. We found no evidence of a relationship between avpr1a microsatellite length and any of our correlates of either social or genetic monogamy in the field. Our results, especially when taken in conjunction with those of recent experimental studies in semi-natural enclosures, suggest that avpr1a polymorphism is unlikely to have been a major influence in the evolution or maintenance of social monogamy in prairie voles under natural conditions. PMID:21442019

Development of microsatellite markers in Lupinus luteus (Fabaceae) and cross-species amplification in other lupine species.

PubMed

Gonzalez, Lorena B Parra; Straub, Shannon C K; Doyle, Jeff J; Ortega, Paula E Mora; Garrido, Haroldo E Salvo; Butler, Iván J Maureira

2010-08-01

Microsatellite primers were developed in Lupinus luteus L., an emerging temperate protein crop, to investigate genetic diversity, population structure, and to facilitate the generation of better yellow lupine varieties. • Thirteen polymorphic primer sets were evaluated in a European and Eastern European accession collection of L. luteus. The primers amplified di-, tri-, and tetranucleotide repeats with 2-4 alleles per locus. These revealed a moderate to low level of genetic variation, as indicated by an average observed heterozygosity of 0.0126. Select loci also amplified successfully in the closely related species L. hispanicus Boiss. & Reut. and in the New World species L. mutabilis Sweet. • These results indicate the utility of primers for the study of genetic diversity across L. luteus populations and related lupine species. The use of these microsatellite markers will facilitate the implementation of several molecular breeding strategies in yellow lupine.

Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness.

PubMed

Telfer, Emily J; Stovold, Grahame T; Li, Yongjun; Silva-Junior, Orzenil B; Grattapaglia, Dario G; Dungey, Heidi S

2015-01-01

Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource

Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and faecal DNA.

PubMed

Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J

2014-11-01

There is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. This is especially important for molecular scatology studies occurring in challenging tropical environments where DNA degrades quickly and the quality of faecal samples varies greatly. We optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using DNA from faeces of wild felids detected by a scat detector dog across Belize in Central America. All microsatellite loci were successfully amplified in the three target species, were polymorphic with average expected heterozygosities of HE = 0.60 ± 0.18 (SD) for jaguars, HE = 0.65 ± 0.21 (SD) for pumas and HE = 0.70 ± 0.13 (SD) for ocelots and had an overall PCR amplification success of 61%. We used this nuclear DNA primer set to successfully identify species and individuals from 49% of 1053 field-collected scat samples. This set of optimized microsatellite multiplexes represents a powerful tool for future efforts to conduct noninvasive studies on multiple, wild Neotropical felids. © 2014 John Wiley & Sons Ltd.

Development and characterization of fourteen novel microsatellite markers for the chestnut short-tailed fruit bat (Carollia castanea), and cross-amplification to related species.

PubMed

Cleary, Katherine A; Waits, Lisette P; Hohenlohe, Paul A

2016-01-01

Rapid anthropogenic land use change threatens the primary habitat of the Chestnut short-tailed bat (Carollia castanea) throughout much of its range. Information on population genetic structure can inform management strategies for this widespread frugivorous bat, and effective protection of C. castanea will also benefit the more than 20 mutualistic plant species of which this bat is the primary seed disperser. To facilitate understanding of population genetic structure in this species, fourteen novel microsatellite markers were developed using restriction-site-associated DNA libraries and Illumina sequencing and tested on 28 individuals from 13 locations in Costa Rica. These are the first microsatellite markers developed for C. castanea. All loci were polymorphic, with number of alleles ranging from 2-11 and average observed heterozygosity of 0.631. Markers were also cross-amplified in three additional frugivorous bat species threatened by habitat loss and fragmentation: Sowell's short-tailed bat (Carollia sowelli), Seba's short-tailed bat (Carollia perspicillata), and the Jamaican fruit bat (Artibeus jamaicensis), and 10, 11, and 8 were polymorphic, respectively.

Development of microsatellite markers for Viscum coloratum (Santalaceae) and their application to wild populations1

PubMed Central

Kim, Bo-Yun; Park, Han-Sol; Kim, Soonok; Kim, Young-Dong

2017-01-01

Premise of the study: Microsatellite primers were developed for Viscum coloratum (Santalaceae), a semiparasitic medicinal plant that is known for its anticancer properties. Due to excessive human harvesting and loss of suitable habitat of its populations, it has become a potentially threatened species requiring immediate conservation efforts. Methods and Results: Based on transcriptome data for V. coloratum, 124 primer pairs were randomly selected for initial validation, of which 19 yielded polymorphic microsatellite loci, with two to six alleles per locus. The usefulness of these markers was assessed for 60 individuals representing three populations of V. coloratum. Observed and expected heterozygosity values ranged from 0.033 to 0.833 and 0.032 to 0.672, respectively. Cross-species amplification for 19 loci in the related species V. album was conducted. Conclusions: The 19 newly developed loci are expected to be useful for studying the population genetics and ecological conservation of V. coloratum. PMID:28090408

Microsatellite markers from the 'South American fruit fly' Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications

PubMed Central

2014-01-01

Background Anastrepha fraterculus Wiedemann is a horticultural pest which causes significant economic losses in the fruit-producing areas of the American continent and limits the access of products to international markets. The use of environmentally friendly control strategies against this pest is constrained due to the limited knowledge of its population structure. Results We developed microsatellite markers for A. fraterculus from four genomic libraries, which were enriched in CA, CAA, GA and CAT microsatellite motifs. Fifty microsatellite regions were evaluated and 14 loci were selected for population genetics studies. Genotypes of 122 individuals sampled from four A. fraterculus populations were analyzed. The level of polymorphism ranged from three to 13 alleles per locus and the mean expected heterozygosity ranged from 0.60 to 0.64. Comparison between allelic and genotypic frequencies showed significant differences among all pairs of populations. Conclusions This novel set of microsatellite markers provides valuable information for the description of genetic variability and population structure of wild populations and laboratory strains of A. fraterculus. This information will be used to identify and characterize candidate strains suitable to implement effective pest control strategies and might represent a first step towards having a more comprehensive knowledge about the genetics of this pest. PMID:25471285

Microsatellite markers for the yam bean Pachyrhizus (Fabaceae).

PubMed

Delêtre, Marc; Soengas, Beatriz; Utge, José; Lambourdière, Josie; Sørensen, Marten

2013-07-01

Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp.) to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus. • Seventeen nuclear simple sequence repeat (SSR) markers with perfect di- and trinucleotide repeats were developed from 454 pyrosequencing of SSR-enriched genomic libraries. Loci were characterized in P. ahipa and wild and cultivated populations of four closely related species. All loci successfully cross-amplified and showed high levels of polymorphism, with number of alleles ranging from three to 12 and expected heterozygosity ranging from 0.095 to 0.831 across the genus. • By enabling rapid assessment of genetic diversity in three native neotropical crops, P. ahipa, P. erosus, and P. tuberosus, and two wild relatives, P. ferrugineus and P. panamensis, these markers will allow exploration of the genetic diversity and evolutionary history of the genus Pachyrhizus.

An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population.

PubMed

Hauser, Lorenz; Baird, Melissa; Hilborn, Ray; Seeb, Lisa W; Seeb, James E

2011-03-01

Because of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high-throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites-that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs (H(E) = 0.30, 80 independent alleles) and 11 microsatellites (H(E) = 0.85, 192 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, although Cervus and SNPPIT detected more parent pairs. Identification of full-sib groups without parental information from relatedness measures was possible using both marker systems, although explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles. © 2011 Blackwell Publishing Ltd.

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides.

PubMed

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-09-01

Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

Development and characterization of microsatellite markers for Brazilian four-eyed frogs (genus Pleurodema) endemic to the Caatinga biome.

PubMed

Thomé, M T C; Alexandrino, J; Lopes, S; Haddad, C F B; Sequeira, F

2014-03-12

We used pyrosequencing to develop microsatellite markers for the Brazilian four-eyed frog Pleurodema diplolister and tested the microsatellite markers for cross-amplification in its sister Pleurodema alium, which are both endemic species of the Caatinga biome in northeastern Brazil. We used multiplex sets to amplify and genotype 30 individuals of P. diplolister from three different populations and 10 individuals of P. alium from a single population. We successfully amplified 24 loci for P. diplolister, 13 of which we were able to amplify in P. alium. All loci were polymorphic. Significant deviations from the Hardy-Weinberg equilibrium and the presence of null alleles were only consistently detected at one locus (Pleu9). These markers will enable the study of geographic genetic diversity and evolutionary processes in these two Caatinga endemics, and the inclusion of genetic data for conservation planning of the Caatinga biome.

Mitochondrial and microsatellite DNA markers reveal a Balkan origin for the highly invasive horse-chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae).

PubMed

Valade, R; Kenis, M; Hernandez-Lopez, A; Augustin, S; Mari Mena, N; Magnoux, E; Rougerie, R; Lakatos, F; Roques, A; Lopez-Vaamonde, C

2009-08-01

Biological invasions usually start with a small number of founder individuals. These founders are likely to represent a small fraction of the total genetic diversity found in the source population. Our study set out to trace genetically the geographical origin of the horse-chestnut leafminer, Cameraria ohridella, an invasive microlepidopteran whose area of origin is still unkown. Since its discovery in Macedonia 25 years ago, this insect has experienced an explosive westward range expansion, progressively colonizing all of Central and Western Europe. We used cytochrome oxidase I sequences (DNA barcode fragment) and a set of six polymorphic microsatellites to assess the genetic variability of C. ohridella populations, and to test the hypothesis that C. ohridella derives from the southern Balkans (Albania, Macedonia and Greece). Analysis of mtDNA of 486 individuals from 88 localities allowed us to identify 25 geographically structured haplotypes. In addition, 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci. High haplotype diversity and low measures of nucleotide diversities including a significantly negative Tajima's D indicate that C. ohridella has experienced rapid population expansion during its dispersal across Europe. Both mtDNA and microsatellites show a reduction in genetic diversity of C. ohridella populations sampled from artificial habitats (e.g. planted trees in public parks, gardens, along roads in urban or sub-urban areas) across Europe compared with C. ohridella sampled in natural stands of horse-chestnuts in the southern Balkans. These findings suggest that European populations of C. ohridella may indeed derive from the southern Balkans.

Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers.

PubMed

Kumar, Vinay; Shukla, Sanjeev K; Mathew, Jose; Sharma, Deepak

2015-01-01

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ▵K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.

Development and characterization of microsatellite markers for the medicinal plant Smilax brasiliensis (Smilacaceae) and related species1

PubMed Central

Martins, Aline R.; Abreu, Aluana G.; Bajay, Miklos M.; Villela, Priscilla M. S.; Batista, Carlos E. A.; Monteiro, Mariza; Alves-Pereira, Alessandro; Figueira, Glyn M.; Pinheiro, José B.; Appezzato-da-Glória, Beatriz; Zucchi, Maria I.

2013-01-01

• Premise of the study: A new set of microsatellite or simple sequence repeat (SSR) markers were developed for Smilax brasiliensis, which is popularly known as sarsaparilla and used in folk medicine as a tonic, antirheumatic, and antisyphilitic. Smilax brasiliensis is sold in Brazilian pharmacies, and its origin and effectiveness are not subject to quality control. • Methods and Results: Using a protocol for genomic library enrichment, primer pairs were developed for 26 microsatellite loci and validated in 17 accessions of S. brasiliensis. Thirteen loci were polymorphic and four were monomorphic. The primers successfully amplified alleles in the congeners S. campestris, S. cissoides, S. fluminensis, S. goyazana, S. polyantha, S. quinquenervia, S. rufescens, S. subsessiliflora, and S. syphilitica. • Conclusions: The new SSR markers described herein are informative tools for genetic diversity and gene flow studies in S. brasiliensis and several congeners. PMID:25202555

Rapid development of microsatellite markers for the endangered fish Schizothorax biddulphi (Günther) using next generation sequencing and cross-species amplification.

PubMed

Luo, Wei; Nie, Zhulan; Zhan, Fanbin; Wei, Jie; Wang, Weimin; Gao, Zexia

2012-11-14

Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The H(o) ranged from 0.15 to 0.83, and H(e) ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis.

Detecting microsatellites within genomes: significant variation among algorithms.

PubMed

Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

2007-04-18

Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker). Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster) spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp), regardless of motif. Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.

Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads

PubMed Central

2013-01-01

Background Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads. Results A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis. Conclusions We show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species

Characterization of microsatellite loci for the pitcher plant midge, Metriocnemus knabi Coq. (Diptera: Chironomidae).

PubMed

Rasic, Gordana; Maxwell, Sheri A; Keyghobadi, Nusha

2009-09-01

As a component of the inquiline community of the purple pitcher plant (Sarracenia purpurea), the pitcher plant midge Metriocneus knabi has been the subject of various ecological studies. However, very little is known about its characteristics beyond the larval stage, in particular the dispersal ability of adults. This study presents new molecular tools developed for testing of evolutionary and ecological questions in natural populations of this species. We describe a set of 12 microsatellite loci specific to M. knabi that are sufficiently polymorphic to provide insight into population genetic structure and dispersal patterns. © 2009 Blackwell Publishing Ltd.

Development of molecular method for sex identification in date palm (Phoenix dactylifera L.) plantlets using novel sex-linked microsatellite markers.

PubMed

Maryam; Jaskani, Muhammad Jafar; Awan, Faisal Saeed; Ahmad, Saeed; Khan, Iqrar A

2016-06-01

Microsatellite markers containing simple sequence repeats (SSRs) are a valuable tool for genetic analysis. Date palm is a dioecious and slow flowering and is very difficult to identify the gender of the trees until it reaches the reproductive age (5-10 years). A total of 12 microsatellite primers were used with 30 date palm samples, 14 parents (8 male + 6 females) and 16 progeny (developed from parents breeding) which showed that microsatellites were highly polymorphic, having a great number of alleles. A total of 124 alleles were characterized in 12 SSR loci. On average, there are 9.08 alleles per locus, with a range from 5 to 16 alleles, for primers mpdCIR15 and mpdCIR57, respectively. These primers produced 15 polymorphic loci specifically in male date palm samples and the seedlings harboring the unique fragments were further characterized as male plants. Increasingly, 38.46 % of these loci were scored as homozygous alleles while 61.53 % heterozygous allelic loci were determined. Primer mpdCIR48 produced a specific locus (250/250) in all male samples whereas the same locus was absent in female samples. Similarly, a locus of 300/310 bp reoccurred in 5 date palm male samples using marker DP-168 which indicated that these are the promising candidate marker to detect the sex in date palm seedlings at early stage. The data resulted from combination of 12 primers enabled the 16 seedling samples progeny (developed from parents breeding) of date palm cultivars to divide into two groups i.e., male and female regarding their sex expression comparative to the parents (male + female) using the principle coordinate analysis.

Detecting microsatellites within genomes: significant variation among algorithms

PubMed Central

Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

2007-01-01

Background Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker). Results Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster) spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp), regardless of motif. Conclusion Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions. PMID:17442102

Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae).

PubMed

Moraes, Evandro M; Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Machado, Marlon C

2012-09-01

The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

Loss of heterozygosity and microsatellite instability in chromosomal segments commonly deleted in squamous cell carcinoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Dyke, D.L.; Worsham, M.J.; Zarbo, R.J.

1994-09-01

To evaluate genetic loss in an unselected series of squamous cell carcinoma (SCC) of the head and neck region (SCCHN), including early stage tumors that do not proliferate aggressively in vitro, we have compared microsatellite repeat polymorphisms (MSRP) in normal blood DNA and tumor DNA from 44 patients with SCCHN, using nine MSRPs from 5q15-q21, proximal 8p, 9p21-p23, 18q21-qter, and 21q21. In previous cytogenetic studies, these chromosome segments were deleted in 40-60% of SCCHN and SCC of the female genital tract. Loss of heterozygosity (LOH) was observed from the ANK1 locus (8p21.1-p11.2) in 2/29 informative tumors. LOH was observed atmore » D5S98 (5q15-5q21) in 5/19, and at D21S11 (21q21) in 5/33 informative tumors. These LOH frequencies were lower than expected, which suggests that the critical region of deletion from these chromosome regions exludes the MSRPs studied here, especially for the 8p MSRP, which may reside in proximal 8p. Alternatively, the observed LOH rates may be appropriate for earlier pathologic stage tumors: total genetic loss increases with tumor stage, and the present study included more stage I and II tumors than did the cytogenetic studies. LOH was observed at D9S126, 1FN, and/or D9S199 (at 9p21, 9p22, & 9p23) in 16/38 informative tumors, and at D18S34 and/or MBP (at 18q21 & 18q22-qter) in 17/39 informative tumors. In addition, three tumors demonstrated microsatellite instability at the MBP locus, and one of these had an expansion at D9S199 as well. This tumor, HFH-SCC-20, also demonstrated microsatellite instability at many other MSRP loci. These results confirm that genetic loss from 9p and 18q is frequent in SCCHN, and demonstrate that microsatellite instability also occurs. Of 66 MSRP changes, 62 were LOH and 4 were microsatellite instabilities. These results also show the usefulness of analyses of MSRP LOH and microsatellite instability in squamous cell carcinoma.« less

Polymorphisms in the canine monoamine oxidase a (MAOA) gene: identification and variation among five broad dog breed groups.

PubMed

Sacco, James; Ruplin, Andrew; Skonieczny, Paul; Ohman, Michael

2017-01-01

In humans, reduced activity of the enzyme monoamine oxidase type A (MAOA) due to genetic polymorphisms within the MAOA gene leads to increased brain neurotransmitter levels associated with aggression. In order to study MAOA genetic diversity in dogs, we designed a preliminary study whose objectives were to identify novel alleles in functionally important regions of the canine MAOA gene, and to investigate whether the frequencies of these polymorphisms varied between five broad breed groups (ancient, herding, mastiff, modern European, and mountain). Fifty dogs representing these five breed groups were sequenced. A total of eleven polymorphisms were found. Seven were single nucleotide polymorphisms (SNPs; two exonic, two intronic and three in the promoter), while four were repeat intronic variations. The most polymorphic loci were repeat regions in introns 1, 2 (7 alleles) and 10 (3 alleles), while the exonic and the promoter regions were highly conserved. Comparison of the allele frequencies of certain microsatellite polymorphisms among the breed groups indicated a decreasing or increasing trend in the number of repeats at different microsatellite loci, as well as the highest genetic diversity for the ancient breeds and the lowest for the most recent mountain breeds, perhaps attributable to canine domestication and recent breed formation. While a specific promoter SNP (-212A > G) is rare in the dog, it is the major allele in wolves. Replacement of this ancestral allele in domestic dogs may lead to the deletion of heat shock factor binding sites on the MAOA promoter. Dogs exhibit significant variation in certain intronic regions of the MAOA gene, while the coding and promoter regions are well-conserved. Distinct genetic differences were observed between breed groups. Further studies are now required to establish whether such polymorphisms are associated in any way with MAOA level and canine behaviour including aggression.

Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

PubMed Central

Arnau, Gemma; MN, Sheela; Chair, Hana; Lebot, Vincent; K, Abraham; Perrier, Xavier; Petro, Dalila; Penet, Laurent; Pavis, Claudie

2017-01-01

Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods. PMID:28355293

[Microsatellite instability and human papilloma virus genotypes in preneoplastic and neoplastic uterine cervix lesions].

PubMed

Roa S, Juan Carlos; Martínez S, Ricardo; Montenegro, Sonia; Roa E, Iván; Capurro V, Italo; Ibacache S, Gilda; Melo A, Angélica

2007-01-01

The association between some specific human papilloma virus (HPV) types and cervix cancer is well known. However, the genetic conditions that favor the development of cervical cancer are less well known. To determine the presence of satellite instability (MSI) in preneoplastic and neoplastic lesions of the cervix and correlate these findings with HPV genotypes. Biopsy samples of cervical lesions were studied. Sixteen had low grade lesions, 22 had high grade lesions and 28 had an epidermoid cancer. Viral types were identified with polymerase chain reaction, dot-blot hybridization and restriction fragment length polymorphism. MSI was determined using a panel of eight highly informative microsatellites. Microsatellite instability in at least one locus was observed in 91, 56 and 69% of low grade lesions, high grade lesions and epidermoid carcinomas, respectively. MSI-High grade, MSI-Low grade instability and microsatellite stability were observed in 5, 60 and 46% of samples, respectively. Two of three samples with high grade instability had HPV 52 genotype. Other viral subtypes had frequencies that ranged from 78% to 100%, with the exception of HPV16 that was present in only 53% of samples with low grade instability. Two thirds of biopsy samples from cervical lesions had MSI, mechanism that can be involved in the first stages of cervical carcinogenesis. The low frequency of high grade instability, its association with HPV52 and the low frequency of HPV16 in samples with low grade instability, suggest different coadjutant mechanisms in cervical carcinogenesis.

Low genetic variation in the MHC class II DRB gene and MHC-linked microsatellites in endangered island populations of the leopard cat (Prionailurus bengalensis) in Japan.

PubMed

Saka, Toshinori; Nishita, Yoshinori; Masuda, Ryuichi

2018-02-01

Isolated populations of the leopard cat (Prionailurus bengalensis) on Tsushima and Iriomote islands in Japan are classified as subspecies P. b. euptilurus and P. b. iriomotensis, respectively. Because both populations have decreased to roughly 100, an understanding of their genetic diversity is essential for conservation. We genotyped MHC class II DRB exon 2 and MHC-linked microsatellite loci to evaluate the diversity of MHC genes in the Tsushima and Iriomote cat populations. We detected ten and four DRB alleles in these populations, respectively. A phylogenetic analysis showed DRB alleles from both populations to be closely related to those in other felid DRB lineages, indicating trans-species polymorphism. The MHC-linked microsatellites were more polymorphic in the Tsushima than in the Iriomote population. The MHC diversity of both leopard cat populations is much lower than in the domestic cat populations on these islands, probably due to inbreeding associated with founder effects, geographical isolation, or genetic drift. Our results predict low resistance of the two endangered populations to new pathogens introduced to the islands.

Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market.

PubMed

Zhao, Jie; Li, Tingting; Zhu, Chao; Jiang, Xiaoling; Zhao, Yan; Xu, Zhenzhen; Yang, Shuming; Chen, Ailiang

2018-06-01

Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.

Effect of chronic administration of mestranol, tamoxifen, and toremifene on hepatic ploidy in rats.

PubMed

Dragan, Y P; Shimel, R J; Bahnub, N; Sattler, G; Vaughan, J R; Jordan, V C; Pitot, H C

1998-06-01

The nonsteroidal antiestrogen tamoxifen increases the incidence of rat liver cancer through a variety of mechanisms. To compare the effects of tamoxifen (TAM) and a structurally similar analog toremifene (TOR) on rat liver, we determined the ploidy distribution for hepatocytes isolated from rats treated for 18 months with these antiestrogens or the estrogenic compound mestranol (MS). Female Sprague-Dawley rats were subjected to a 70% partial hepatectomy and administered the solvent, trioctanoin, or diethylnitrosamine (10 mg DEN/kg). After a 2-week recovery from the surgery, the rats were administered a basal diet or one containing TAM (250 or 500 ppm), TOR (250, 500, or 750 ppm), or MS (0.2 ppm) for 18 months. Pathologic changes in the liver were examined in the 15-22 rats per treatment group at the 18-month time point. An increased incidence of hepatocellular carcinomas (HCC) was detected in the 500 ppm TAM group, but not with the other treatments that did not include DEN. Both TOR and TAM promoted formation of DEN-initiated HCCs. At sacrifice, four to five rats per group were perfused and the hepatocytes isolated and cultured. Karyotypic analysis was performed on colcemid-blocked cells after 2 days in culture. The hepatic ploidy distribution was characterized in Giemsa-stained metaphase spreads. These studies indicated that chronic treatment with TAM alone resulted in a shift from tetraploid to diploid, as was also observed for rats treated once with DEN. TOR and MS alone did not cause this change in hepatic ploidy at the doses examined. A shift toward an increased content of diploid hepatocytes occurred in all rats treated once with DEN followed by TAM, TOR, or MS. These results indicate that tamoxifen administration results in a shift toward growth of diploid hepatocytes, thus contributing to its carcinogenic action in the rat liver.

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides1

PubMed Central

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-01-01

Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species. PMID:26421250

Identification of cardiomyocyte nuclei and assessment of ploidy for the analysis of cell turnover.

PubMed

Bergmann, Olaf; Zdunek, Sofia; Alkass, Kanar; Druid, Henrik; Bernard, Samuel; Frisén, Jonas

2011-01-15

Assays to quantify myocardial renewal rely on the accurate identification of cardiomyocyte nuclei. We previously ¹⁴C birth dated human cardiomyocytes based on the nuclear localization of cTroponins T and I. A recent report by Kajstura et al. suggested that cTroponin I is only localized to the nucleus in a senescent subpopulation of cardiomyocytes, implying that ¹⁴C birth dating of cTroponin T and I positive cell populations underestimates cardiomyocyte renewal in humans. We show here that the isolation of cell nuclei from the heart by flow cytometry with antibodies against cardiac Troponins T and I, as well as pericentriolar material 1 (PCM-1), allows for isolation of close to all cardiomyocyte nuclei, based on ploidy and marker expression. We also present a reassessment of cardiomyocyte ploidy, which has important implications for the analysis of cell turnover, and iododeoxyuridine (IdU) incorporation data. These data provide the foundation for reliable analysis of cardiomyocyte turnover in humans. Copyright © 2010 Elsevier Inc. All rights reserved.

Isolation and characterization of eight novel microsatellite loci in the double-crested cormorant (Phalacrocorax auritus)

USGS Publications Warehouse

Mercer, Dacey; Haig, Susan; Mullins, Thomas

2010-01-01

We describe the isolation and characterization of eight microsatellite loci from the double-crested cormorant (Phalacrocorax auritus). Genetic variability was assessed using 60 individuals from three populations. All loci were variable with the number of alleles ranging from two to 17 per locus, and observed heterozygosity varying from 0.05 to 0.89. No loci showed signs of linkage disequilibrium and all loci conformed to Hardy–Weinberg equilibrium frequencies. Further, all loci amplified and were polymorphic in two related Phalacrocorax species. These loci should prove useful for population genetic studies of the double-crested cormorant and other pelecaniform species.

Development of microsatellite markers in Caryophyllaeus laticeps (Cestoda: Caryophyllidea), monozoic fish tapeworm, using next-generation sequencing approach.

PubMed

Králová-Hromadová, Ivica; Minárik, Gabriel; Bazsalovicsová, Eva; Mikulíček, Peter; Oravcová, Alexandra; Pálková, Lenka; Hanzelová, Vladimíra

2015-02-01

Caryophyllaeus laticeps (Pallas 1781) (Cestoda: Caryophyllidea) is a monozoic tapeworm of cyprinid fishes with a distribution area that includes Europe, most of the Palaearctic Asia and northern Africa. Broad geographic distribution, wide range of definitive fish hosts and recently revealed high morphological plasticity of the parasite, which is not in an agreement with molecular findings, make this species to be an interesting model for population biology studies. Microsatellites (short tandem repeat (STR) markers), as predominant markers for population genetics, were designed for C. laticeps using a next-generation sequencing (NGS) approach. Out of 165 marker candidates, 61 yielded PCR products of the expected size and in 25 of the candidates a declared repetitive motif was confirmed by Sanger sequencing. After the fragment analysis, six loci were proved to be polymorphic and tested for heterozygosity, Hardy-Weinberg equilibrium and the presence of null alleles on 59 individuals coming from three geographically widely separated populations (Slovakia, Russia and UK). The number of alleles in particular loci and populations ranged from two to five. Significant deficit of heterozygotes and the presence of null alleles were found in one locus in all three populations. Other loci showed deviations from Hardy-Weinberg equilibrium and the presence of null alleles only in some populations. In spite of relatively low polymorphism and the potential presence of null alleles, newly developed microsatellites may be applied as suitable markers in population genetic studies of C. laticeps.

Reproduction at the extremes: pseudovivipary, hybridization and genetic mosaicism in Posidonia australis (Posidoniaceae).

PubMed

Sinclair, Elizabeth A; Statton, John; Hovey, Renae; Anthony, Janet M; Dixon, Kingsley W; Kendrick, Gary A

2016-02-01

Organisms occupying the edges of natural geographical ranges usually survive at the extreme limits of their innate physiological tolerances. Extreme and prolonged fluctuations in environmental conditions, often associated with climate change and exacerbated at species' geographical range edges, are known to trigger alternative responses in reproduction. This study reports the first observations of adventitious inflorescence-derived plantlet formation in the marine angiosperm Posidonia australis, growing at the northern range edge (upper thermal and salinity tolerance) in Shark Bay, Western Australia. These novel plantlets are described and a combination of microsatellite DNA markers and flow cytometry is used to determine their origin. Polymorphic microsatellite DNA markers were used to generate multilocus genotypes to determine the origin of the adventitious inflorescence-derived plantlets. Ploidy and genome size were estimated using flow cytometry. All adventitious plantlets were genetically identical to the maternal plant and were therefore the product of a novel pseudoviviparous reproductive event. It was found that 87 % of the multilocus genotypes contained three alleles in at least one locus. Ploidy was identical in all sampled plants. The genome size (2 C value) for samples from Shark Bay and from a separate site much further south was not significantly different, implying they are the same ploidy level and ruling out a complete genome duplication (polyploidy). Survival at range edges often sees the development of novel responses in the struggle for survival and reproduction. This study documents a physiological response at the trailing edge, whereby reproductive strategy can adapt to fluctuating conditions and suggests that the lower-than-usual water temperature triggered unfertilized inflorescences to 'switch' to growing plantlets that were adventitious clones of their maternal parent. This may have important long-term implications as both genetic and

Novel microsatellite markers for the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) and effects of null alleles on population genetics analyses.

PubMed

Song, W; Cao, L-J; Wang, Y-Z; Li, B-Y; Wei, S-J

2017-06-01

The oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) is an important economic pest of stone and pome fruits worldwide. We sequenced the OFM genome using next-generation sequencing and characterized the microsatellite distribution. In total, 56,674 microsatellites were identified, with 11,584 loci suitable for primer design. Twenty-seven polymorphic microsatellites, including 24 loci with trinucleotide repeat and three with pentanucleotide repeat, were validated in 95 individuals from four natural populations. The allele numbers ranged from 4 to 40, with an average value of 13.7 per locus. A high frequency of null alleles was observed in most loci developed for the OFM. Three marker panels, all of the loci, nine loci with the lowest null allele frequencies, and nine loci with the highest null allele frequencies, were established for population genetics analyses. The null allele influenced estimations of genetic diversity parameters but not the OFM's genetic structure. Both a STRUCTURE analysis and a discriminant analysis of principal components, using the three marker panels, divided the four natural populations into three groups. However, more individuals were incorrectly assigned by the STRUCTURE analysis when the marker panel with the highest null allele frequency was used compared with the other two panels. Our study provides empirical research on the effects of null alleles on population genetics analyses. The microsatellites developed will be valuable markers for genetic studies of the OFM.

Development and Application of Transcriptome-Derived Microsatellites in Actinidia eriantha (Actinidiaceae)

PubMed Central

Guo, Rui; Landis, Jacob B.; Moore, Michael J.; Meng, Aiping; Jian, Shuguang; Yao, Xiaohong; Wang, Hengchang

2017-01-01

Actinidia eriantha Benth. is a diploid perennial woody vine native to China and is recognized as a valuable species for commercial kiwifruit improvement with high levels of ascorbic acid as well as having been used in traditional Chinese medicine. Due to the lack of genomic resources for the species, microsatellite markers for population genetics studies are scarce. In this study, RNASeq was conducted on fruit tissue of A. eriantha, yielding 5,678,129 reads with a total output of 3.41 Gb. De novo assembly yielded 69,783 non-redundant unigenes (41.3 Mb), of which 21,730 were annotated using protein databases. A total of 8,658 EST-SSR loci were identified in 7,495 unigene sequences, for which primer pairs were successfully designed for 3,842 loci (44.4%). Among these, 183 primer pairs were assayed for PCR amplification, yielding 69 with detectable polymorphism in A. eriantha. Additionally, 61 of the 69 polymorphic loci could be successfully amplified in at least one other Actinidia species. Of these, 14 polymorphic loci (mean NA = 6.07 ± 2.30) were randomly selected for assessing levels of genetic diversity and population structure within A. eriantha. Finally, a neighbor-joining tree and Bayesian clustering analysis showed distinct clustering into two groups (K = 2), agreeing with the geographical distributions of these populations. Overall, our results will facilitate further studies of genetic diversity within A. eriantha and will aid in discriminating outlier loci involved in local adaptation. PMID:28890721

Verification and characterization of chromosome duplication in haploid maize.

PubMed

de Oliveira Couto, E G; Resende Von Pinho, E V; Von Pinho, R G; Veiga, A D; de Carvalho, M R; de Oliveira Bustamante, F; Nascimento, M S

2015-06-26

Doubled haploid technology has been used by various private companies. However, information regarding chromosome duplication methodologies, particularly those concerning techniques used to identify duplication in cells, is limited. Thus, we analyzed and characterized artificially doubled haploids using microsatellites molecular markers, pollen viability, and flow cytometry techniques. Evaluated material was obtained using two different chromosome duplication protocols in maize seeds considered haploids, resulting from the cross between the haploid inducer line KEMS and 4 hybrids (GNS 3225, GNS 3032, GNS 3264, and DKB 393). Fourteen days after duplication, plant samples were collected and assessed by flow cytometry. Further, the plants were transplanted to a field, and samples were collected for DNA analyses using microsatellite markers. The tassels were collected during anthesis for pollen viability analyses. Haploid, diploid, and mixoploid individuals were detected using flow cytometry, demonstrating that this technique was efficient for identifying doubled haploids. The microsatellites markers were also efficient for confirming the ploidies preselected by flow cytometry and for identifying homozygous individuals. Pollen viability showed a significant difference between the evaluated ploidies when the Alexander and propionic-carmin stains were used. The viability rates between the plodies analyzed show potential for fertilization.

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites.

PubMed

Li, Muwang; Shen, Li; Xu, Anying; Miao, Xuexia; Hou, Chengxiang; Sun, Pingjiang; Zhang, Yuehua; Huang, Yongping

2005-10-01

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2-17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12-0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species

PubMed Central

Diekmann, Kerstin; Hodkinson, Trevor R.; Barth, Susanne

2012-01-01

Background and Aims Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne ‘Cashel’. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Methods Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. Key Results All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A8 mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. Conclusions The new markers are a valuable tool for plant breeding companies, seed testing

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species.

PubMed

Diekmann, Kerstin; Hodkinson, Trevor R; Barth, Susanne

2012-11-01

Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to

Short communication: development and characterization of novel transcriptome-derived microsatellites for genetic analysis of persimmon.

PubMed

Luo, C; Zhang, Q L; Luo, Z R

2014-04-16

Oriental persimmon (Diospyros kaki Thunb.) (2n = 6x = 90) is a major commercial and deciduous fruit tree that is believed to have originated in China. However, rare transcriptomic and genomic information on persimmon is available. Using Roche 454 sequencing technology, the transcriptome from RNA of the flowers of D. kaki was analyzed. A total of 1,250,893 reads were generated and 83,898 unigenes were assembled. A total of 42,711 SSR loci were identified from 23,494 unigenes and 289 polymerase chain reaction primer pairs were designed. Of these 289 primers, 155 (53.6%) showed robust PCR amplification and 98 revealed polymorphism between 15 persimmon genotypes, indicating a polymorphic rate of 63.23% of the productive primers for characterization and genotyping of the genus Diospyros. Transcriptome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no genomic sequence information available.

Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers.

PubMed

Gulsen, Osman; Sever-Mutlu, Songul; Mutlu, Nedim; Tuna, Metin; Karaguzel, Osman; Shearman, Robert C; Riordan, Terrance P; Heng-Moss, Tiffany M

2009-05-01

Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P < 0.001). The AMOVA results indicated that 91 and 94% of the total variation resided within ploidy level and provinces, respectively. The UPGMA analysis suggested that commercial bermudagrass cultivars only one-third of the available genetic variation. SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems. Elucidating Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars.

Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae).

PubMed

Pfeiffer, Tanja; Roschanski, Anna M; Pannell, John R; Korbecka, Grazyna; Schnittler, Martin

2011-01-01

For many applications in population genetics, codominant simple sequence repeats (SSRs) may have substantial advantages over dominant anonymous markers such as amplified fragment length polymorphisms (AFLPs). In high polyploids, however, allele dosage of SSRs cannot easily be determined and alleles are not easily attributable to potentially diploidized loci. Here, we argue that SSRs may nonetheless be better than AFLPs for polyploid taxa if they are analyzed as effectively dominant markers because they are more reliable and more precise. We describe the transfer of SSRs developed for diploid Mercurialis huetii to the clonal dioecious M. perennis. Primers were tested on a set of 54 male and female plants from natural decaploid populations. Eight of 65 tested loci produced polymorphic fragments. Binary profiles from 4 different scoring routines were used to define multilocus lineages (MLLs). Allowing for fragment differences within 1 MLL, all analyses revealed the same 14 MLLs without conflicting with merigenet, sex, or plot assignment. For semiautomatic scoring, a combination of as few as 2 of the 4 most polymorphic loci resulted in unambiguous discrimination of clones. Our study demonstrates that microsatellite fingerprinting of polyploid plants is a cost efficient and reliable alternative to AFLPs, not least because fewer loci are required than for diploids.

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

PubMed Central

Doorduin, Leonie; Gravendeel, Barbara; Lammers, Youri; Ariyurek, Yavuz; Chin-A-Woeng, Thomas; Vrieling, Klaas

2011-01-01

Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing. PMID:21444340

Flow cytometry, microsatellites and niche models reveal the origins and geographical structure of Alnus glutinosa populations in Europe

PubMed Central

Mandák, Bohumil; Vít, Petr; Krak, Karol; Trávníček, Pavel; Havrdová, Alena; Hadincová, Věroslava; Zákravský, Petr; Jarolímová, Vlasta; Bacles, Cecile Fanny Emilie; Douda, Jan

2016-01-01

Background and Aims Polyploidy in plants has been studied extensively. In many groups, two or more cytotypes represent separate biological entities with distinct distributions, histories and ecology. This study examines the distribution and origins of cytotypes of Alnus glutinosa in Europe, North Africa and western Asia. Methods A combined approach was used involving flow cytometry and microsatellite analysis of 12 loci in 2200 plants from 209 populations combined with species distribution modelling using MIROC and CCSM climatic models, in order to analyse (1) ploidy and genetic variation, (2) the origin of tetraploid A. glutinosa, considering A. incana as a putative parent, and (3) past distributions of the species. Key Results The occurrence of tetraploid populations of A. glutinosa in Europe is determined for the first time. The distribution of tetraploids is far from random, forming two geographically well-delimited clusters located in the Iberian Peninsula and the Dinaric Alps. Based on microsatellite analysis, both tetraploid clusters are probably of autopolyploid origin, with no indication that A. incana was involved in their evolutionary history. A projection of the MIROC distribution model into the Last Glacial Maximum (LGM) showed that (1) populations occurring in the Iberian Peninsula and North Africa were probably interconnected during the LGM and (2) populations occurring in the Dinaric Alps did not exist throughout the last glacial periods, having retreated southwards into lowland areas of the Balkan Peninsula. Conclusions Newly discovered tetraploid populations are situated in the putative main glacial refugia, and neither of them was likely to have been involved in the colonization of central and northern Europe after glacial withdrawal. This could mean that neither the Iberian Peninsula nor the western part of the Balkan Peninsula served as effective refugial areas for northward post-glacial expansion of A. glutinosa. PMID:26467247

In vitro susceptibility to quinine and microsatellite variations of the Plasmodium falciparum Na+/H+ exchanger (Pfnhe-1) gene: the absence of association in clinical isolates from the Republic of Congo

PubMed Central

2011-01-01

Background Quinine is still recommended as an effective therapy for severe cases of Plasmodium falciparum malaria, but the parasite has developed resistance to the drug in some cases. Investigations into the genetic basis for quinine resistance (QNR) suggest that QNR is complex and involves several genes, with either an additive or a pairwise effect. The results obtained when assessing one of these genes, the plasmodial Na+/H+ exchanger, Pfnhe-1, were found to depend upon the geographic origin of the parasite strain. Most of the associations identified have been made in Asian strains; in contrast, in African strains, the influence of Pfnhe on QNR is not apparent. However, a recent study carried out in Kenya did show a significant association between a Pfnhe polymorphism and QNR. As genetic differences may exist across the African continent, more field data are needed to determine if this association exists in other African regions. In the present study, association between Pfnhe and QNR is investigated in a series of isolates from central Africa. Methods The sequence analysis of the polymorphisms at the Pfnhe-1 ms4760 microsatellite and the evaluation of in vitro quinine susceptibility (by isotopic assay) were conducted in 74 P. falciparum isolates from the Republic of Congo. Results Polymorphisms in the number of DNNND or NHNDNHNNDDD repeats in the Pfnhe-1 ms4760 microsatellite were not associated with quinine susceptibility. Conclusions The polymorphism in the microsatellite ms4760 in Pfnhe-1 that cannot be used to monitor quinine response in the regions of the Republic of Congo, where the isolates came from. This finding suggests that there exists a genetic background associated with geographic area for the association that will prevent the use of Pfnhe as a molecular marker for QNR. The contribution of Pfnhe to the in vitro response to quinine remains to be assessed in other regions, including in countries with different levels of drug pressure. PMID:21314947

DNA Ploidy Measured on Archived Pretreatment Biopsy Material May Correlate With Prostate-Specific Antigen Recurrence After Prostate Brachytherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keyes, Mira, E-mail: mkeyes@bccancer.bc.ca; MacAulay, Calum; Hayes, Malcolm

Purpose: To explore whether DNA ploidy of prostate cancer cells determined from archived transrectal ultrasound-guided biopsy specimens correlates with disease-free survival. Methods and Materials: Forty-seven failures and 47 controls were selected from 1006 consecutive low- and intermediate-risk patients treated with prostate {sup 125}I brachytherapy (July 1998-October 2003). Median follow-up was 7.5 years. Ten-year actuarial disease-free survival was 94.1%. Controls were matched using age, initial prostate-specific antigen level, clinical stage, Gleason score, use of hormone therapy, and follow-up (all P nonsignificant). Seventy-eight specimens were successfully processed; 27 control and 20 failure specimens contained more than 100 tumor cells were used formore » the final analysis. The Feulgen-Thionin stained cytology samples from archived paraffin blocks were used to determine the DNA ploidy of each tumor by measuring integrated optical densities. Results: The samples were divided into diploid and aneuploid tumors. Aneuploid tumors were found in 16 of 20 of the failures (80%) and 8 of 27 controls (30%). Diploid DNA patients had a significantly lower rate of disease recurrence (P=.0086) (hazard ratio [HR] 0.256). On multivariable analysis, patients with aneuploid tumors had a higher prostate-specific antigen failure rate (HR 5.13). Additionally, those with “excellent” dosimetry (V100 >90%; D90 >144 Gy) had a significantly lower recurrence rate (HR 0.25). All patients with aneuploid tumors and dosimetry classified as “nonexcellent” (V100 <90%; D90 <144 Gy) (5 of 5) had disease recurrence, compared with 40% of patients with aneuploid tumors and “excellent” dosimetry (8 of 15). In contrast, dosimetry did not affect the outcome for diploid patients. Conclusions: Using core biopsy material from archived paraffin blocks, DNA ploidy correctly classified the majority of failures and nonfailures in this study. The results suggest that DNA ploidy can be used

Development and characterization of microsatellite markers for Berberis thunbergii (Berberidaceae).

PubMed

Allen, Jenica M; Obae, Samuel G; Brand, Mark H; Silander, John A; Jones, Kenneth L; Nunziata, Schyler O; Lance, Stacey L

2012-05-01

Microsatellite markers were isolated and characterized in Berberis thunbergii, an invasive and ornamental shrub in the eastern United States, to assess genetic diversity among populations and potentially identify horticultural cultivars. A total of 12 loci were identified for the species. Eight of the loci were polymorphic and were screened in 24 individuals from two native (Tochigi and Ibaraki prefectures, Japan) and one invasive (Connecticut, USA) population and 21 horticultural cultivars. The number of alleles per locus ranged from three to seven, and observed heterozygosity ranged from 0.048 to 0.636. These new markers will provide tools for examining genetic relatedness of B. thunbergii plants in the native and invasive range, including phylogeographic studies and assessment of rapid evolution in the invasive range. These markers may also provide tools for examining hybridization with other related species in the invasive range.

Identification and characterization of microsatellites from calafate (Berberis microphylla, Berberidaceae).

PubMed

Varas, Benjamín; Castro, María H; Rodriguez, Roberto; von Baer, Dietrich; Mardones, Claudia; Hinrichsen, Patricio

2013-07-01

Southern barberry or calafate (Berberis microphylla) is a shrub species endemic to the Patagonian region of South America that is used for human consumption. The fruit is very rich in vitamin C and anthocyanins and has a very high antioxidant capacity. There have been only a few genetic studies of this and other closely related species. • Here we present the first 18 microsatellite markers of B. microphylla that were characterized using 66 accessions of calafate from Patagonia. On average, they had 7.6 alleles per marker, with an expected heterozygosity of 0.688. The informativeness of these markers was also evaluated in another 15 Berberis species, including most of the native and endemic Chilean species. • The results confirm that these new simple sequence repeat markers are very polymorphic and potentially useful in genetic studies in any species of the genus Berberis.

Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome.

PubMed

Pramod, Sreepriya; Perkins, Andy D; Welch, Mark E

2014-08-01

The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly 5'UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli.

Novel microsatellite loci for studies of Thamnophis Gartersnake genetic identity and hybridization

USGS Publications Warehouse

Sloss, Brian L.; Schuurman, Gregor W.; Paloski, Rori A.; Boyle, Owen D.; Kapfer, Joshua M.

2012-01-01

Butler’s Gartersnakes (BGS; Thamnophis butleri) are confined to open and semi-open canopy wetlands and adjacent uplands, habitats under threat of development in Wisconsin. To address issues of species identity and putative hybridization with congeneric snakes, a suite of 18 microsatellite loci capable of cross-species amplification of Plains Gartersnakes (T. radix) and Common Gartersnakes (T. sirtalis) was developed. All loci were polymorphic in BGS with mean number of alleles per locus of 16.11 (range = 3–41) and mean observed heterozygosity of 0.659 (range = 0.311–0.978). Loci amplified efficiently in the congeneric species with high levels of intra- and inter-specific variation. These loci will aid ongoing efforts to effectively identify and manage BGS in Wisconsin.

A suite of microsatellite markers optimized for amplification of DNA from Addax (Addax nasomaculatus) blood preserved on FTA cards.

PubMed

Heim, Brett C; Ivy, Jamie A; Latch, Emily K

2012-01-01

The addax (Addax nasomaculatus) is a critically endangered antelope that is currently maintained in zoos through regional, conservation breeding programs. As for many captive species, incomplete pedigree data currently impedes the ability of addax breeding programs to confidently manage the genetics of captive populations and to select appropriate animals for reintroduction. Molecular markers are often used to improve pedigree resolution, thereby improving the long-term effectiveness of genetic management. When developing a suite of molecular markers, it is important to consider the source of DNA, as the utility of markers may vary across DNA sources. In this study, we optimized a suite of microsatellite markers for use in genotyping captive addax blood samples collected on FTA cards. We amplified 66 microsatellite loci previously described in other Artiodactyls. Sixteen markers amplified a single product in addax, but only 5 of these were found to be polymorphic in a sample of 37 addax sampled from a captive herd at Fossil Rim Wildlife Center in the US. The suite of microsatellite markers developed in this study provides a new tool for the genetic management of captive addax, and demonstrates that FTA cards can be a useful means of sample storage, provided appropriate loci are used in downstream analyses. © 2011 Wiley Periodicals, Inc.